Title: Interact with Data on 'SurveyCTO'
Description: 'SurveyCTO' is a platform for mobile data collection in offline settings.
The 'rsurveycto' R package uses the 'SurveyCTO' REST API
<https://docs.surveycto.com/05-exporting-and-publishing-data/05-api-access/01.api-access.html>
to read datasets and forms from a 'SurveyCTO' server into R as 'data.table's
and to download file attachments. The package also has limited support to
write datasets to a server.
Author: Jake Hughey [aut, cre],
Robert On [aut]
Maintainer: Jake Hughey <jakejhughey@gmail.com>
Diff between rsurveycto versions 0.0.5 dated 2022-09-08 and 0.1.0 dated 2022-09-26
DESCRIPTION | 12 +- MD5 | 35 ++++--- NAMESPACE | 9 ++ R/scto_auth.R | 41 ++++++++- R/scto_get_attachments.R | 1 R/scto_meta.R |only R/scto_read.R | 129 +++++++++++------------------ R/scto_read_utils.R |only R/scto_write.R | 49 ++++++++--- R/utils.R | 71 +++++++++++---- man/scto_auth.Rd | 3 man/scto_meta.Rd |only man/scto_quiet.Rd |only man/scto_read.Rd | 26 ++++- man/scto_write.Rd | 31 +++++- tests/testthat/test-scto-auth.R | 11 ++ tests/testthat/test-scto-get-attachments.R | 4 tests/testthat/test-scto-meta.R |only tests/testthat/test-scto-read.R | 15 ++- tests/testthat/test-scto-write.R | 56 +++++++++--- tests/testthat/test-utils.R | 11 -- 21 files changed, 320 insertions(+), 184 deletions(-)
Title: Automated Grading of R Scripts
Description: Tools for grading the coding style and documentation of R
scripts. This is the R component of Roger the Omni Grader, an
automated grading system for computer programming projects based on
Unix shell scripts; see <https://gitlab.com/roger-project>. The
package also provides an R interface to the shell scripts. Inspired by
the lintr package.
Author: Vincent Goulet [aut, cre],
Samuel Frechette [aut],
Jean-Christophe Langlois [aut],
Jim Hester [ctb]
Maintainer: Vincent Goulet <vincent.goulet@act.ulaval.ca>
Diff between roger versions 1.0-0 dated 2022-08-25 and 1.1-0 dated 2022-09-26
DESCRIPTION | 8 +++--- MD5 | 12 ++++----- NAMESPACE | 2 - R/documentation.R | 26 +++++++++++++++++++++ inst/NEWS.Rd | 9 +++++++ man/documentation.Rd | 40 ++++++++++++++++++++++----------- tests/documentation-tests.R | 53 +++++++++++++++++++++++++++++++++++++------- 7 files changed, 118 insertions(+), 32 deletions(-)
Title: Visualization of a Correlation Matrix using 'ggplot2'
Description: The 'ggcorrplot' package can be used to visualize easily a
correlation matrix using 'ggplot2'. It provides a solution for
reordering the correlation matrix and displays the significance level
on the plot. It also includes a function for computing a matrix of
correlation p-values.
Author: Alboukadel Kassambara [aut, cre],
Indrajeet Patil [ctb]
Maintainer: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>
Diff between ggcorrplot versions 0.1.3 dated 2019-05-19 and 0.1.4 dated 2022-09-26
DESCRIPTION | 48 ++++++++++++++-------- MD5 | 37 +++++++++-------- NEWS.md | 69 ++++++++++++++++++++++++++------ R/ggcorrplot.R | 78 +++++++++++++++++++++++-------------- README.md | 66 ++++++++++++++++++++----------- inst/WORDLIST | 11 ++++- man/ggcorrplot.Rd | 53 ++++++++++++++++++------- tests/spelling.R | 5 +- tests/testthat |only tests/testthat.R |only tools/README-demo-ggcorrplot-1.png |binary tools/README-demo-ggcorrplot-2.png |binary tools/README-demo-ggcorrplot-3.png |binary tools/README-demo-ggcorrplot-4.png |binary tools/README-demo-ggcorrplot-5.png |binary tools/README-demo-ggcorrplot-6.png |binary tools/README-demo-ggcorrplot-7.png |binary tools/README-demo-ggcorrplot-8.png |binary tools/README-demo-ggcorrplot-9.png |binary 19 files changed, 250 insertions(+), 117 deletions(-)
Title: Relative Simulator
Description: A set of tools to explore the behaviour statistics used for forensic DNA interpretation when close relatives are involved. The package also offers some useful tools for exploring other forensic DNA situations.
Author: James M. Curran
Maintainer: James M. Curran <j.curran@auckland.ac.nz>
Diff between relSim versions 0.3-3 dated 2022-09-15 and 0.3-4 dated 2022-09-26
DESCRIPTION | 8 ++++---- MD5 | 9 +++++---- R/concatProfiles.R |only R/readProfiles.R | 20 ++++++++++++++++---- man/readProfiles.Rd | 2 +- src/relSim.cpp | 17 ++++++++++------- 6 files changed, 36 insertions(+), 20 deletions(-)
Title: Paginate the HTML Output of R Markdown with CSS for Print
Description: Use the paged media properties in CSS and the JavaScript
library 'paged.js' to split the content of an HTML document into discrete
pages. Each page can have its page size, page numbers, margin boxes, and
running headers, etc. Applications of this package include books, letters,
reports, papers, business cards, resumes, and posters.
Author: Yihui Xie [aut, cre] ,
Romain Lesur [aut, cph] ,
Brent Thorne [aut] ,
Xianying Tan [aut] ,
Christophe Dervieux [ctb] ,
Atsushi Yasumoto [ctb] ,
RStudio, PBC [cph],
Adam Hyde [ctb] ,
Min-Zhong Lu [ctb] ,
Zulko [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between pagedown versions 0.18 dated 2022-04-26 and 0.19 dated 2022-09-26
DESCRIPTION | 6 +++--- LICENSE | 2 +- MD5 | 12 ++++++------ NEWS.md | 6 +++++- R/chrome.R | 2 +- inst/resources/css/default.css | 2 +- man/chrome_print.Rd | 2 +- 7 files changed, 18 insertions(+), 14 deletions(-)
Title: Functions for Tabular Reporting
Description: Create pretty tables for 'HTML', 'PDF', 'Microsoft Word', 'Microsoft PowerPoint'
documents from 'R Markdown' and as 'Grid Graphics' objects. Functions are provided to let users
create tables, modify and format their content. It also extends package 'officer' that does
not contain any feature for customized tabular reporting.
Author: David Gohel [aut, cre],
Clementine Jager [ctb],
Panagiotis Skintzos [aut],
Quentin Fazilleau [ctb],
Maxim Nazarov [ctb] ,
Titouan Robert [ctb],
Michael Barrowman [ctb] ,
Atsushi Yasumoto [ctb] ,
Paul Julian [ctb] ,
Sean Browning [ctb] ,
Remi Theriaul [...truncated...]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between flextable versions 0.8.1 dated 2022-09-19 and 0.8.2 dated 2022-09-26
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 7 +++++++ R/as_flextable_tabulator.R | 2 +- man/tabulator_colnames.Rd | 10 +++++----- tests/testthat/test-captions-rmd.R | 2 ++ 6 files changed, 23 insertions(+), 14 deletions(-)
Title: Estimation and Additional Tools for Alternative Shared Frailty
Models
Description: Provide estimation and data generation tools for some new multivariate frailty models.
This version includes the gamma, inverse Gaussian and weighted Lindley as the distribution
for the frailty terms.
For the basal model, it is considered a parametric approach based on the Weibull distribution
and a semiparametric approach. For details, see Gallardo and Bourguignon (2022)
<arXiv:2206.12973>.
Author: Diego Gallardo [aut, cre],
Marcelo Bourguignon [aut]
Maintainer: Diego Gallardo <diego.gallardo@uda.cl>
Diff between extrafrail versions 1.1 dated 2022-08-06 and 1.2 dated 2022-09-26
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 4 ++++ R/summary.extrafrail.R | 2 +- 4 files changed, 12 insertions(+), 8 deletions(-)
Title: Analyzing Partial Rankings in Networks
Description: Implements methods for centrality related analyses of networks.
While the package includes the possibility to build more than 20 indices,
its main focus lies on index-free assessment of centrality via partial
rankings obtained by neighborhood-inclusion or positional dominance. These
partial rankings can be analyzed with different methods, including
probabilistic methods like computing expected node ranks and relative
rank probabilities (how likely is it that a node is more central than another?).
The methodology is described in depth in the vignettes and in
Schoch (2018) <doi:10.1016/j.socnet.2017.12.003>.
Author: David Schoch [aut, cre] ,
Julian Mueller [ctb]
Maintainer: David Schoch <david@schochastics.net>
Diff between netrankr versions 1.1.1 dated 2021-12-21 and 1.2.0 dated 2022-09-26
netrankr-1.1.1/netrankr/man/figures |only netrankr-1.2.0/netrankr/DESCRIPTION | 8 netrankr-1.2.0/netrankr/LICENSE | 4 netrankr-1.2.0/netrankr/MD5 | 73 - netrankr-1.2.0/netrankr/NEWS.md | 5 netrankr-1.2.0/netrankr/R/approximate.ranks.R | 4 netrankr-1.2.0/netrankr/R/get.rankings.R | 2 netrankr-1.2.0/netrankr/R/indirect.relations.R | 8 netrankr-1.2.0/netrankr/R/mcmc.rank.R | 6 netrankr-1.2.0/netrankr/R/rank.analysis.R | 20 netrankr-1.2.0/netrankr/R/utils.R | 10 netrankr-1.2.0/netrankr/README.md | 12 netrankr-1.2.0/netrankr/build/vignette.rds |binary netrankr-1.2.0/netrankr/inst/CITATION | 13 netrankr-1.2.0/netrankr/inst/doc/benchmarks.Rmd | 12 netrankr-1.2.0/netrankr/inst/doc/benchmarks.html | 308 +++++++ netrankr-1.2.0/netrankr/inst/doc/centrality_indices.html | 284 ++++++- netrankr-1.2.0/netrankr/inst/doc/indirect_relations.html | 276 ++++++ netrankr-1.2.0/netrankr/inst/doc/neighborhood_inclusion.html | 310 +++++++ netrankr-1.2.0/netrankr/inst/doc/partial_centrality.Rmd | 2 netrankr-1.2.0/netrankr/inst/doc/partial_centrality.html | 267 ++++++ netrankr-1.2.0/netrankr/inst/doc/positional_dominance.html | 272 ++++++ netrankr-1.2.0/netrankr/inst/doc/probabilistic_cent.html | 319 +++++++ netrankr-1.2.0/netrankr/inst/doc/threshold_graph.html | 329 +++++++- netrankr-1.2.0/netrankr/inst/doc/use_case.html | 439 +++++++++-- netrankr-1.2.0/netrankr/man/exact_rank_prob.Rd | 2 netrankr-1.2.0/netrankr/man/get_rankings.Rd | 2 netrankr-1.2.0/netrankr/src/checkPairs.cpp | 8 netrankr-1.2.0/netrankr/src/listingIdeals.cpp | 2 netrankr-1.2.0/netrankr/vignettes/benchmarks.Rmd | 12 netrankr-1.2.0/netrankr/vignettes/mcmc_samples_exp.png |binary netrankr-1.2.0/netrankr/vignettes/mcmc_samples_rel.png |binary netrankr-1.2.0/netrankr/vignettes/partial_centrality.Rmd | 2 netrankr-1.2.0/netrankr/vignettes/quality_expected_mse.png |binary netrankr-1.2.0/netrankr/vignettes/quality_relative_mse.png |binary netrankr-1.2.0/netrankr/vignettes/runtimes_exact.png |binary 36 files changed, 2677 insertions(+), 334 deletions(-)
Title: Manipulate Date, POSIXct and hms Vectors
Description: Manipulates date ('Date'), date time ('POSIXct') and time
('hms') vectors. Date/times are considered discrete and are floored
whenever encountered. Times are wrapped and time zones are maintained
unless explicitly altered by the user.
Author: Joe Thorley [aut] ,
Ayla Pearson [aut, cre] ,
Poisson Consulting [cph, fnd]
Maintainer: Ayla Pearson <ayla@poissonconsulting.ca>
Diff between dttr2 versions 0.4.1 dated 2022-08-26 and 0.4.2 dated 2022-09-26
DESCRIPTION | 26 +++++++++++++------------- MD5 | 8 ++++---- NEWS.md | 15 +++++++++++++++ man/dttr2-package.Rd | 7 ++++++- tests/testthat/test-check.R | 2 +- 5 files changed, 39 insertions(+), 19 deletions(-)
Title: Calculation of the Integrated Flow of Particles Between Polygons
Description: Calculate the flow of particles between polygons by two integration methods:
integration by a cubature method and integration on a grid of points.
Annie Bouvier, Kien Kieu, Kasia Adamczyk and Herve Monod (2009)
<doi:10.1016/j.envsoft.2008.11.006>.
Author: Annie Bouvier [aut, cph],
Kien Kieu [aut, cph],
Kasia Adamczyk [aut, cph],
Herve Monod [aut, cph],
Jean-Francois Rey [cre]
Maintainer: Jean-Francois Rey <jean-francois.rey@inrae.fr>
Diff between RCALI versions 0.3.3 dated 2022-08-12 and 0.3.4 dated 2022-09-26
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- src/intersection.cc | 4 ++-- src/readPoly.cc | 6 +++--- 4 files changed, 12 insertions(+), 12 deletions(-)
Title: A Multi-Process 'dplyr' Backend
Description: Partition a data frame across multiple worker processes to
provide simple multicore parallelism.
Author: Hadley Wickham [aut, cre],
RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between multidplyr versions 0.1.1 dated 2021-12-01 and 0.1.2 dated 2022-09-26
DESCRIPTION | 36 ++-- MD5 | 20 +- NEWS.md | 5 R/cluster-call.R | 85 ++++++++-- README.md | 24 +- build/vignette.rds |binary inst/doc/multidplyr.html | 288 ++++++++++++++++++++-------------- man/cluster_call.Rd | 18 +- man/multidplyr-package.Rd | 2 tests/testthat/_snaps/cluster-call.md | 34 +++- tests/testthat/test-cluster-call.R | 34 +++- 11 files changed, 366 insertions(+), 180 deletions(-)
Title: Create Constraints for Small Test Assembly Problems
Description: Provides simple functions to create constraints for small test assembly problems
(e.g. van der Linden (2005, ISBN: 978-0-387-29054-6)) using sparse matrices. Currently,
'GLPK', 'lpSolve', 'Symphony', and 'Gurobi' are supported as solvers. The 'gurobi' package is not available from
any mainstream repository; see <https://www.gurobi.com/downloads/>.
Author: Benjamin Becker [aut, cre],
Dries Debeer [aut]
Maintainer: Benjamin Becker <b.becker@iqb.hu-berlin.de>
Diff between eatATA versions 1.0.0 dated 2021-07-06 and 1.1.0 dated 2022-09-26
eatATA-1.0.0/eatATA/man/calculateExpectedRT.Rd |only eatATA-1.1.0/eatATA/DESCRIPTION | 8 eatATA-1.1.0/eatATA/MD5 | 116 eatATA-1.1.0/eatATA/NAMESPACE | 6 eatATA-1.1.0/eatATA/NEWS.md | 11 eatATA-1.1.0/eatATA/R/appendSolution.R | 2 eatATA-1.1.0/eatATA/R/calculateExpectedRT.R | 82 eatATA-1.1.0/eatATA/R/get_mean_var_3PLN.R |only eatATA-1.1.0/eatATA/R/inspectSolution.R | 2 eatATA-1.1.0/eatATA/R/itemCategoryMinMaxConstraint.R | 224 eatATA-1.1.0/eatATA/R/itemTuples.R | 3 eatATA-1.1.0/eatATA/R/itemValuesConstraint.R | 8 eatATA-1.1.0/eatATA/R/itemValuesMinMaxConstraint.R | 220 eatATA-1.1.0/eatATA/R/objectives.R | 4 eatATA-1.1.0/eatATA/README.md | 16 eatATA-1.1.0/eatATA/build/eatATA.pdf | 5761 +++++----- eatATA-1.1.0/eatATA/build/partial.rdb |only eatATA-1.1.0/eatATA/inst/doc/minimal_example.html | 359 eatATA-1.1.0/eatATA/inst/doc/overview.Rmd | 2 eatATA-1.1.0/eatATA/inst/doc/overview.html | 402 eatATA-1.1.0/eatATA/inst/doc/use_case_pilot_study.html | 495 eatATA-1.1.0/eatATA/man/acrossFormsConstraint.Rd | 156 eatATA-1.1.0/eatATA/man/analyzeBlockExclusion.Rd | 138 eatATA-1.1.0/eatATA/man/analyzeComplexBlockExclusion.Rd | 88 eatATA-1.1.0/eatATA/man/appendSolution.Rd | 88 eatATA-1.1.0/eatATA/man/autoItemValuesMinMaxConstraint.Rd | 102 eatATA-1.1.0/eatATA/man/calculateIIF.Rd | 86 eatATA-1.1.0/eatATA/man/cappedMaximinObjective.Rd | 100 eatATA-1.1.0/eatATA/man/combineConstraints.Rd | 52 eatATA-1.1.0/eatATA/man/computeTargetValues.Rd | 252 eatATA-1.1.0/eatATA/man/depletePoolConstraint.Rd | 52 eatATA-1.1.0/eatATA/man/dummiesToFactor.Rd | 68 eatATA-1.1.0/eatATA/man/getMean3PLN.Rd |only eatATA-1.1.0/eatATA/man/get_mean_3PLN.Rd |only eatATA-1.1.0/eatATA/man/inspectSolution.Rd | 114 eatATA-1.1.0/eatATA/man/itemCategoryConstraint.Rd | 108 eatATA-1.1.0/eatATA/man/itemCategoryRangeConstraint.Rd | 226 eatATA-1.1.0/eatATA/man/itemExclusionConstraint.Rd | 164 eatATA-1.1.0/eatATA/man/itemTuples.Rd | 78 eatATA-1.1.0/eatATA/man/itemUsageConstraint.Rd | 142 eatATA-1.1.0/eatATA/man/itemValuesConstraint.Rd | 132 eatATA-1.1.0/eatATA/man/itemValuesRangeConstraint.Rd | 210 eatATA-1.1.0/eatATA/man/itemsPerFormConstraint.Rd | 98 eatATA-1.1.0/eatATA/man/items_diao.Rd | 54 eatATA-1.1.0/eatATA/man/items_lsa.Rd | 54 eatATA-1.1.0/eatATA/man/items_mini.Rd | 44 eatATA-1.1.0/eatATA/man/items_pilot.Rd | 48 eatATA-1.1.0/eatATA/man/items_vera.Rd | 48 eatATA-1.1.0/eatATA/man/matrixExclusionTuples.Rd | 68 eatATA-1.1.0/eatATA/man/maxObjective.Rd | 84 eatATA-1.1.0/eatATA/man/maximinObjective.Rd | 94 eatATA-1.1.0/eatATA/man/minObjective.Rd | 84 eatATA-1.1.0/eatATA/man/minimaxObjective.Rd | 94 eatATA-1.1.0/eatATA/man/stemInclusionTuples.Rd | 72 eatATA-1.1.0/eatATA/man/useSolver.Rd | 130 eatATA-1.1.0/eatATA/tests/testthat/test_acrossFormsConstraint.R | 130 eatATA-1.1.0/eatATA/tests/testthat/test_calculateExpectedRT.R | 43 eatATA-1.1.0/eatATA/tests/testthat/test_get_mean_var_3PLN.R |only eatATA-1.1.0/eatATA/tests/testthat/test_itemTuples.R | 12 eatATA-1.1.0/eatATA/tests/testthat/test_itemValuesConstraint.R | 5 eatATA-1.1.0/eatATA/tests/testthat/test_stemInclusionTuples.R | 11 eatATA-1.1.0/eatATA/vignettes/overview.Rmd | 2 62 files changed, 6215 insertions(+), 5037 deletions(-)
Title: Climate Variability Indices for Ecological Modelling
Description: Supports analysis of trends in climate change,
ecological and crop modelling.
Author: Kaue de Sousa [aut, cre] ,
Jacob van Etten [ctb, ths] ,
Svein O. Solberg [ctb, ths]
Maintainer: Kaue de Sousa <desousa.kaue@gmail.com>
Diff between climatrends versions 0.2 dated 2022-02-24 and 0.4 dated 2022-09-26
DESCRIPTION | 15 - LICENSE | 4 MD5 | 20 +- NEWS.md | 5 R/get_timeseries.R | 17 -- R/internal_functions.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Overview.html | 374 +++++++++++++++++++++++++++++++++++++++++----- man/climatrends.Rd | 2 vignettes/climatrends.bib | 1 11 files changed, 374 insertions(+), 66 deletions(-)
Title: Accessing Spatial Basemaps in R
Description: A lightweight package to access spatial basemaps from open sources such as 'OpenStreetMap', 'Carto', 'Mapbox' and others in R.
Author: Jakob Schwalb-Willmann [aut, cre]
Maintainer: Jakob Schwalb-Willmann <dev@schwalb-willmann.de>
Diff between basemaps versions 0.0.4 dated 2022-09-08 and 0.0.5 dated 2022-09-26
DESCRIPTION | 15 +- MD5 | 26 ++- NAMESPACE | 36 ++--- NEWS.md | 20 +++ R/basemap.R | 178 +++++++++++++++------------ R/internal.R | 270 +++++++++++++++++++++++++---------------- R/plot.R |only README.md | 187 ++++++++++++++++------------ man/basemap.Rd | 45 ++++-- man/plot.Rd |only tests/testthat/helper-vars.R | 19 ++ tests/testthat/test-basemap.R | 56 +++++--- tests/testthat/test-cache.R |only tests/testthat/test-draw_ext.R | 5 tests/testthat/test-internal.R | 13 + tests/testthat/test-plot.R |only 16 files changed, 532 insertions(+), 338 deletions(-)
Title: Take Screenshots of Web Pages
Description: Takes screenshots of web pages, including Shiny applications and R
Markdown documents.
Author: Winston Chang [aut, cre],
Yihui Xie [ctb],
Francois Guillem [ctb],
Barret Schloerke [ctb],
Nicolas Perriault [ctb]
Maintainer: Winston Chang <winston@rstudio.com>
Diff between webshot versions 0.5.3 dated 2022-04-14 and 0.5.4 dated 2022-09-26
DESCRIPTION | 9 +++++---- MD5 | 10 ++++++---- NEWS.md | 5 +++++ R/utils.R | 2 +- README.md | 7 +++---- tests |only 6 files changed, 20 insertions(+), 13 deletions(-)
Title: Dynamic Function-Oriented 'Make'-Like Declarative Workflows
Description: As a pipeline toolkit for Statistics and data science in R,
the 'targets' package brings together function-oriented programming and
'Make'-like declarative workflows.
It analyzes the dependency relationships among the tasks of a workflow,
skips steps that are already up to date, runs the necessary
computation with optional parallel workers, abstracts files as
R objects, and provides tangible evidence that the results match
the underlying code and data. The methodology in this package
borrows from GNU 'Make' (2015, ISBN:978-9881443519)
and 'drake' (2018, <doi:10.21105/joss.00550>).
Author: William Michael Landau [aut, cre]
,
Matthew T. Warkentin [ctb],
Mark Edmondson [ctb] ,
Samantha Oliver [rev] ,
Tristan Mahr [rev] ,
Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@gmail.com>
Diff between targets versions 0.13.4 dated 2022-09-15 and 0.13.5 dated 2022-09-26
DESCRIPTION | 6 - MD5 | 116 ++++++++++++++--------------- NEWS.md | 6 + R/tar_built.R | 4 - R/tar_canceled.R | 4 - R/tar_delete.R | 2 R/tar_errored.R | 4 - R/tar_glimpse.R | 2 R/tar_invalidate.R | 2 R/tar_load.R | 4 - R/tar_load_raw.R | 2 R/tar_make.R | 4 - R/tar_manifest.R | 4 - R/tar_meta.R | 6 - R/tar_network.R | 2 R/tar_newer.R | 4 - R/tar_objects.R | 4 - R/tar_older.R | 4 - R/tar_outdated.R | 2 R/tar_process.R | 2 R/tar_progress.R | 4 - R/tar_sitrep.R | 4 - R/tar_skipped.R | 4 - R/tar_started.R | 4 - R/tar_visnetwork.R | 2 R/tar_watch_server.R | 2 inst/run/run.R | 2 man/tar_built.Rd | 4 - man/tar_canceled.Rd | 4 - man/tar_delete.Rd | 2 man/tar_errored.Rd | 4 - man/tar_glimpse.Rd | 4 - man/tar_invalidate.Rd | 2 man/tar_load.Rd | 4 - man/tar_load_raw.Rd | 2 man/tar_make.Rd | 4 - man/tar_make_clustermq.Rd | 4 - man/tar_make_future.Rd | 4 - man/tar_manifest.Rd | 4 - man/tar_mermaid.Rd | 2 man/tar_meta.Rd | 6 - man/tar_network.Rd | 2 man/tar_newer.Rd | 4 - man/tar_objects.Rd | 4 - man/tar_older.Rd | 4 - man/tar_outdated.Rd | 2 man/tar_process.Rd | 2 man/tar_progress.Rd | 4 - man/tar_sitrep.Rd | 4 - man/tar_skipped.Rd | 4 - man/tar_started.Rd | 4 - man/tar_visnetwork.Rd | 4 - tests/interactive/test-tar_poll.R | 2 tests/interactive/test-time.R | 12 +-- tests/testthat/test-class_file.R | 2 tests/testthat/test-tar_manifest.R | 4 - tests/testthat/test-tar_newer.R | 2 tests/testthat/test-tar_older.R | 2 tests/testthat/test-tar_progress_summary.R | 2 59 files changed, 164 insertions(+), 156 deletions(-)
Title: Nonparametric Spearman's Correlation for Survival Data
Description: Nonparametric estimation of Spearman's rank correlation with bivariate survival (right-censored) data as described in Eden, S.K., Li, C., Shepherd B.E. (2021), Nonparametric Estimation of Spearman's Rank Correlation with Bivariate Survival Data, Biometrics (under revision). The package also provides functions that visualize bivariate survival data and bivariate probability mass function.
Author: Svetlana Eden [aut, cre],
Chun Li [aut, anl],
Bryan Shepherd [aut, anl]
Maintainer: Svetlana Eden <svetlana.k.eden.1@vumc.org>
Diff between survSpearman versions 1.0.0 dated 2021-01-29 and 1.0.1 dated 2022-09-26
DESCRIPTION | 6 MD5 | 6 NEWS.md | 3 inst/doc/survSpearman.html | 1066 +++++++++++++++++++++------------------------ 4 files changed, 523 insertions(+), 558 deletions(-)
Title: Statistical Inference in High Dimensional Regression
Description: Inference procedures in the high-dimensional setting for
(1) linear functionals in generalized linear regression ('Cai et al.' (2019) <arXiv:1904.12891>, 'Guo et al.' (2020) <arXiv:2012.07133>, 'Cai et al.' (2021)),
(2) individual treatment effects in generalized linear regression,
(3) quadratic functionals in generalized linear regression ('Guo et al.' (2019) <arXiv:1909.01503>).
Author: Prabrisha Rakshit, Zhenyu Wang, Tony Cai, Zijian Guo
Maintainer: Zijian Guo <zijguo@stat.rutgers.edu>
Diff between SIHR versions 1.0.1 dated 2022-08-10 and 1.1.0 dated 2022-09-26
SIHR-1.0.1/SIHR/R/Projection_Directions.R |only SIHR-1.0.1/SIHR/inst |only SIHR-1.1.0/SIHR/DESCRIPTION | 10 - SIHR-1.1.0/SIHR/MD5 | 26 +- SIHR-1.1.0/SIHR/NAMESPACE | 46 ++-- SIHR-1.1.0/SIHR/R/ITE.R | 133 +++++++------ SIHR-1.1.0/SIHR/R/LF.R | 251 ++++++++++++++----------- SIHR-1.1.0/SIHR/R/Methods.R | 28 +- SIHR-1.1.0/SIHR/R/QF.R | 291 ++++++++++++++++++------------ SIHR-1.1.0/SIHR/R/check.R | 55 ++--- SIHR-1.1.0/SIHR/R/helpers.R | 112 ++++++++++- SIHR-1.1.0/SIHR/README.md | 273 +++++++++++++++++----------- SIHR-1.1.0/SIHR/man/ITE.Rd | 102 +++++----- SIHR-1.1.0/SIHR/man/LF.Rd | 80 +++----- SIHR-1.1.0/SIHR/man/QF.Rd | 94 ++++----- 15 files changed, 871 insertions(+), 630 deletions(-)
Title: Testing for Shiny Applications
Description: Automated unit testing of Shiny applications through a headless 'Chromium' browser.
Author: Barret Schloerke [cre, aut] ,
RStudio [cph, fnd],
Winston Chang [ctb] ,
Gabor Csardi [ctb] ,
Hadley Wickham [ctb] ,
Mango Solutions [cph, ccp]
Maintainer: Barret Schloerke <barret@rstudio.com>
Diff between shinytest2 versions 0.1.1 dated 2022-09-06 and 0.2.0 dated 2022-09-26
shinytest2-0.1.1/shinytest2/tests/testthat/_snaps |only shinytest2-0.1.1/shinytest2/tests/testthat/test-aaa.R |only shinytest2-0.1.1/shinytest2/tests/testthat/test-duplicate-ids.R |only shinytest2-0.1.1/shinytest2/tests/testthat/test-shiny-app-driver.R |only shinytest2-0.2.0/shinytest2/DESCRIPTION | 34 shinytest2-0.2.0/shinytest2/MD5 | 182 +- shinytest2-0.2.0/shinytest2/NAMESPACE | 3 shinytest2-0.2.0/shinytest2/NEWS.md | 97 + shinytest2-0.2.0/shinytest2/R/app-driver-expect-download.R | 105 + shinytest2-0.2.0/shinytest2/R/app-driver-expect-js.R | 9 shinytest2-0.2.0/shinytest2/R/app-driver-expect-screenshot.R | 24 shinytest2-0.2.0/shinytest2/R/app-driver-expect-values.R | 6 shinytest2-0.2.0/shinytest2/R/app-driver-get-log.R | 4 shinytest2-0.2.0/shinytest2/R/app-driver-initialize.R | 54 shinytest2-0.2.0/shinytest2/R/app-driver-set-inputs.R | 3 shinytest2-0.2.0/shinytest2/R/app-driver-start.R | 2 shinytest2-0.2.0/shinytest2/R/app-driver-stop.R | 25 shinytest2-0.2.0/shinytest2/R/app-driver-timeout.R |only shinytest2-0.2.0/shinytest2/R/app-driver-upload-file.R | 3 shinytest2-0.2.0/shinytest2/R/app-driver-wait.R | 11 shinytest2-0.2.0/shinytest2/R/app-driver.R | 405 +++--- shinytest2-0.2.0/shinytest2/R/chromote-methods.R | 38 shinytest2-0.2.0/shinytest2/R/compare-screenshot-threshold.R |only shinytest2-0.2.0/shinytest2/R/cpp11.R |only shinytest2-0.2.0/shinytest2/R/expect-snapshot.R | 2 shinytest2-0.2.0/shinytest2/R/httr.R | 4 shinytest2-0.2.0/shinytest2/R/migrate.R | 11 shinytest2-0.2.0/shinytest2/R/platform.R | 2 shinytest2-0.2.0/shinytest2/R/record-test.R | 7 shinytest2-0.2.0/shinytest2/R/shinytest2-logs.R | 2 shinytest2-0.2.0/shinytest2/R/shinytest2-package.R |only shinytest2-0.2.0/shinytest2/R/test-app.R | 170 ++ shinytest2-0.2.0/shinytest2/R/use.R | 24 shinytest2-0.2.0/shinytest2/R/utils.R | 10 shinytest2-0.2.0/shinytest2/README.md | 1 shinytest2-0.2.0/shinytest2/build/vignette.rds |binary shinytest2-0.2.0/shinytest2/inst/WORDLIST |only shinytest2-0.2.0/shinytest2/inst/doc/in-depth.R | 8 shinytest2-0.2.0/shinytest2/inst/doc/in-depth.Rmd | 11 shinytest2-0.2.0/shinytest2/inst/doc/in-depth.html | 32 shinytest2-0.2.0/shinytest2/inst/doc/robust.R | 4 shinytest2-0.2.0/shinytest2/inst/doc/robust.Rmd | 236 +-- shinytest2-0.2.0/shinytest2/inst/doc/robust.html | 209 +-- shinytest2-0.2.0/shinytest2/inst/doc/shinytest2.R | 16 shinytest2-0.2.0/shinytest2/inst/doc/shinytest2.Rmd | 14 shinytest2-0.2.0/shinytest2/inst/doc/shinytest2.html | 10 shinytest2-0.2.0/shinytest2/inst/doc/use-application-audit.R |only shinytest2-0.2.0/shinytest2/inst/doc/use-application-audit.Rmd |only shinytest2-0.2.0/shinytest2/inst/doc/use-application-audit.html |only shinytest2-0.2.0/shinytest2/inst/doc/use-ci.Rmd | 19 shinytest2-0.2.0/shinytest2/inst/doc/use-ci.html | 25 shinytest2-0.2.0/shinytest2/inst/doc/use-package.R | 2 shinytest2-0.2.0/shinytest2/inst/doc/use-package.Rmd | 17 shinytest2-0.2.0/shinytest2/inst/doc/use-package.html | 19 shinytest2-0.2.0/shinytest2/inst/doc/using-monkey-testing.R | 12 shinytest2-0.2.0/shinytest2/inst/doc/using-monkey-testing.Rmd | 218 ++- shinytest2-0.2.0/shinytest2/inst/doc/using-monkey-testing.html | 135 +- shinytest2-0.2.0/shinytest2/inst/doc/z-migration.Rmd | 41 shinytest2-0.2.0/shinytest2/inst/doc/z-migration.html | 94 - 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Title: Reactivity Visualizer for 'shiny'
Description: Building interactive web applications with R is incredibly easy
with 'shiny'. Behind the scenes, 'shiny' builds a reactive graph that can
quickly become intertwined and difficult to debug. 'reactlog'
(Schloerke 2019) <doi:10.5281/zenodo.2591517> provides a visual insight into
that black box of 'shiny' reactivity by constructing a directed dependency
graph of the application's reactive state at any time point in a reactive
recording.
Author: Barret Schloerke [aut, cre] ,
Joe Cheng [ctb],
RStudio [cph, fnd]
Maintainer: Barret Schloerke <barret@rstudio.com>
Diff between reactlog versions 1.1.0 dated 2020-09-12 and 1.1.1 dated 2022-09-26
DESCRIPTION | 14 MD5 | 22 - NEWS.md | 10 R/shinyModule.R | 2 R/showReactLog.R | 2 README.md | 6 build/vignette.rds |binary inst/doc/reactlog.R | 4 inst/doc/reactlog.Rmd | 8 inst/doc/reactlog.html | 615 +++++++++++++++++++++++--------- inst/reactlog/reactlogAsset/reactlog.js | 16 vignettes/reactlog.Rmd | 8 12 files changed, 494 insertions(+), 213 deletions(-)
Title: Linked Micromap Plots for U. S. and Other Geographic Areas
Description: Provides the users with the ability to quickly create
linked micromap plots for a collection of geographic areas.
Linked micromap plots are visualizations of geo-referenced data
that link statistical graphics to an organized series of small
maps or graphic images. The Help description contains examples
of how to use the 'micromapST' function. Contained in this
package are border group datasets to support creating linked
micromap plots for the 50 U.S. states and District of Columbia
(51 areas), the U. S. 20 Seer Registries, the 105 counties in
the state of Kansas, the 62 counties of New York, the 24
counties of Maryland, the 29 counties of Utah, the 32
administrative areas in China, the 218 administrative areas in
the UK and Ireland (for testing only), the 25 districts in the
city of Seoul South Korea, and the 52 counties on the Africa
continent.
A border group dataset contains the boundaries related to the
data level areas, a second layer boundaries, a top or third
layer boundary, a pa [...truncated...]
Author: Jim Pearson [aut, cre, cph],
Dan Carr [aut, cph],
Linda Pickle [ctb, cph]
Maintainer: Jim Pearson <jbpearson353@gmail.com>
Diff between micromapST versions 2.0.0 dated 2022-08-20 and 2.0.1 dated 2022-09-26
micromapST-2.0.0/micromapST/data/KY_ADD.rda |only micromapST-2.0.0/micromapST/data/KY_ADD_BG.rda |only micromapST-2.0.0/micromapST/data/Ky_ADD_LungCancer_2006_2010.rda |only micromapST-2.0.0/micromapST/man/KY_ADD.Rd |only micromapST-2.0.0/micromapST/man/KY_ADD_BG.Rd |only micromapST-2.0.0/micromapST/man/Ky_ADD_LungCancer_2006_2010.Rd |only micromapST-2.0.1/micromapST/DESCRIPTION | 14 micromapST-2.0.1/micromapST/MD5 | 49 micromapST-2.0.1/micromapST/NAMESPACE | 3 micromapST-2.0.1/micromapST/R/BuildBorderGroup.r | 2465 ++++--- micromapST-2.0.1/micromapST/R/globals.r | 33 micromapST-2.0.1/micromapST/R/micromapDefSets.r | 536 - micromapST-2.0.1/micromapST/R/micromapST.r | 3243 +++++----- micromapST-2.0.1/micromapST/R/panelFunctions.r | 246 micromapST-2.0.1/micromapST/data/ChinaBG.rda |binary micromapST-2.0.1/micromapST/data/USSeerBG.rda |binary micromapST-2.0.1/micromapST/data/cnPopData.rda |binary micromapST-2.0.1/micromapST/inst/doc/NEWS | 6 micromapST-2.0.1/micromapST/man/BuildBorderGroup.Rd | 73 micromapST-2.0.1/micromapST/man/ChinaBG.Rd | 6 micromapST-2.0.1/micromapST/man/PlotVis.Rd |only micromapST-2.0.1/micromapST/man/bordGrp.Rd | 12 micromapST-2.0.1/micromapST/man/detailsVariables.Rd | 3 micromapST-2.0.1/micromapST/man/messages-BG.Rd | 892 +- micromapST-2.0.1/micromapST/man/messages-MM.Rd | 374 - micromapST-2.0.1/micromapST/man/micromapGDefaults.Rd | 1021 +-- micromapST-2.0.1/micromapST/man/micromapGSetDefaults.Rd | 3 micromapST-2.0.1/micromapST/man/micromapST-package.Rd | 26 micromapST-2.0.1/micromapST/man/micromapST.Rd | 122 29 files changed, 4916 insertions(+), 4211 deletions(-)
Title: Decision Analytic Modelling in Health Economics
Description: Classes and functions for modelling health care interventions
using decision trees and semi-Markov models. Mechanisms are provided for
associating an uncertainty distribution with each source variable and for
ensuring transparency of the mathematical relationships between variables.
The package terminology follows Briggs "Decision Modelling for Health
Economic Evaluation" (2006, ISBN:978-0-19-852662-9).
Author: Andrew Sims [aut, cre] ,
Kim Fairbairn [aut] ,
Paola Cognigni [aut]
Maintainer: Andrew Sims <andrew.sims@newcastle.ac.uk>
Diff between rdecision versions 1.1.2 dated 2022-09-07 and 1.1.3 dated 2022-09-26
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rdecision-1.1.3/rdecision/R/ExprModVar.R | 165 +- rdecision-1.1.3/rdecision/R/GammaDistribution.R | 97 - rdecision-1.1.3/rdecision/R/GammaModVar.R | 11 rdecision-1.1.3/rdecision/R/Graph.R | 106 - rdecision-1.1.3/rdecision/R/LeafNode.R | 7 rdecision-1.1.3/rdecision/R/LogNormDistribution.R | 105 - rdecision-1.1.3/rdecision/R/LogNormModVar.R | 11 rdecision-1.1.3/rdecision/R/MarkovState.R | 8 rdecision-1.1.3/rdecision/R/ModVar.R | 96 - rdecision-1.1.3/rdecision/R/Node.R | 25 rdecision-1.1.3/rdecision/R/NormModVar.R | 8 rdecision-1.1.3/rdecision/R/NormalDistribution.R | 71 - rdecision-1.1.3/rdecision/R/Reaction.R | 105 - rdecision-1.1.3/rdecision/R/SemiMarkovModel.R | 431 ++---- rdecision-1.1.3/rdecision/R/Stack.R | 16 rdecision-1.1.3/rdecision/R/Transition.R | 57 rdecision-1.1.3/rdecision/R/data.R | 3 rdecision-1.1.3/rdecision/R/utils.R | 64 rdecision-1.1.3/rdecision/README.md | 46 rdecision-1.1.3/rdecision/inst/CITATION | 3 rdecision-1.1.3/rdecision/inst/NEWS.md | 30 rdecision-1.1.3/rdecision/inst/doc/DT00-DecisionTreeTutorial.R | 108 - rdecision-1.1.3/rdecision/inst/doc/DT00-DecisionTreeTutorial.Rmd | 112 - rdecision-1.1.3/rdecision/inst/doc/DT00-DecisionTreeTutorial.html | 241 +-- rdecision-1.1.3/rdecision/inst/doc/DT01-Sumatriptan.R | 10 rdecision-1.1.3/rdecision/inst/doc/DT01-Sumatriptan.Rmd | 10 rdecision-1.1.3/rdecision/inst/doc/DT01-Sumatriptan.html | 20 rdecision-1.1.3/rdecision/inst/doc/DT02-Tegaderm.R | 212 +-- rdecision-1.1.3/rdecision/inst/doc/DT02-Tegaderm.Rmd | 212 +-- rdecision-1.1.3/rdecision/inst/doc/DT02-Tegaderm.html | 327 ++-- rdecision-1.1.3/rdecision/inst/doc/DT03-ShaleGas.R | 52 rdecision-1.1.3/rdecision/inst/doc/DT03-ShaleGas.Rmd | 53 rdecision-1.1.3/rdecision/inst/doc/DT03-ShaleGas.html | 46 rdecision-1.1.3/rdecision/inst/doc/GT01-NewScientistPuzzle.R | 110 - rdecision-1.1.3/rdecision/inst/doc/GT01-NewScientistPuzzle.Rmd | 118 + rdecision-1.1.3/rdecision/inst/doc/GT01-NewScientistPuzzle.html | 52 rdecision-1.1.3/rdecision/inst/doc/SM01-HIV.R | 171 +- rdecision-1.1.3/rdecision/inst/doc/SM01-HIV.Rmd | 173 +- rdecision-1.1.3/rdecision/inst/doc/SM01-HIV.html | 152 +- rdecision-1.1.3/rdecision/man/Action.Rd | 26 rdecision-1.1.3/rdecision/man/Arborescence.Rd | 6 rdecision-1.1.3/rdecision/man/Arrow.Rd | 6 rdecision-1.1.3/rdecision/man/BriggsEx47.Rd | 3 rdecision-1.1.3/rdecision/man/DecisionTree.Rd | 32 rdecision-1.1.3/rdecision/man/Digraph.Rd | 4 rdecision-1.1.3/rdecision/man/DiracDistribution.Rd | 50 rdecision-1.1.3/rdecision/man/Distribution.Rd | 27 rdecision-1.1.3/rdecision/man/ExprModVar.Rd | 4 rdecision-1.1.3/rdecision/man/GammaModVar.Rd | 2 rdecision-1.1.3/rdecision/man/Graph.Rd | 2 rdecision-1.1.3/rdecision/man/ModVar.Rd | 2 rdecision-1.1.3/rdecision/man/Reaction.Rd | 22 rdecision-1.1.3/rdecision/man/SemiMarkovModel.Rd | 7 rdecision-1.1.3/rdecision/man/Stack.Rd | 3 rdecision-1.1.3/rdecision/man/Transition.Rd | 6 rdecision-1.1.3/rdecision/man/figures/README-sb.gv |only rdecision-1.1.3/rdecision/man/figures/README-sb.png |only rdecision-1.1.3/rdecision/tests/testthat.R | 1 rdecision-1.1.3/rdecision/tests/testthat/setup.R | 13 rdecision-1.1.3/rdecision/tests/testthat/test-Action.R | 33 rdecision-1.1.3/rdecision/tests/testthat/test-Arborescence.R | 178 +- rdecision-1.1.3/rdecision/tests/testthat/test-Arrow.R | 20 rdecision-1.1.3/rdecision/tests/testthat/test-BetaDistribution.R | 60 rdecision-1.1.3/rdecision/tests/testthat/test-BetaModVar.R | 84 - 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rdecision-1.1.3/rdecision/tests/testthat/test-MarkovState.R | 40 rdecision-1.1.3/rdecision/tests/testthat/test-ModVar.R | 69 rdecision-1.1.3/rdecision/tests/testthat/test-Node.R | 6 rdecision-1.1.3/rdecision/tests/testthat/test-NormModVar.R | 64 rdecision-1.1.3/rdecision/tests/testthat/test-NormalDistribution.R | 37 rdecision-1.1.3/rdecision/tests/testthat/test-Reaction.R | 43 rdecision-1.1.3/rdecision/tests/testthat/test-SemiMarkovModel.R | 359 ++--- rdecision-1.1.3/rdecision/tests/testthat/test-Stack.R | 42 rdecision-1.1.3/rdecision/tests/testthat/test-Transition.R | 50 rdecision-1.1.3/rdecision/tests/testthat/test-utils.R | 131 + rdecision-1.1.3/rdecision/vignettes/DT00-DecisionTreeTutorial.Rmd | 112 - rdecision-1.1.3/rdecision/vignettes/DT01-Sumatriptan.Rmd | 10 rdecision-1.1.3/rdecision/vignettes/DT02-Tegaderm.Rmd | 212 +-- rdecision-1.1.3/rdecision/vignettes/DT03-ShaleGas.Rmd | 53 rdecision-1.1.3/rdecision/vignettes/GT01-NewScientistPuzzle.Rmd | 118 + rdecision-1.1.3/rdecision/vignettes/SM01-HIV.Rmd | 173 +- 118 files changed, 4825 insertions(+), 4631 deletions(-)
Title: Estimating and Testing Intergenerational Social Mobility Effect
Description: Estimate and test inter-generational social mobility effect on an outcome with cross-sectional or longitudinal data.
Author: Jiahui Xu [aut, cre],
Liying Luo [aut]
Maintainer: Jiahui Xu <jpx5053@psu.edu>
Diff between MCM versions 0.1.6 dated 2022-09-25 and 0.1.7 dated 2022-09-26
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/mcm.R | 4 ++-- tests/mcm_package_test.R | 6 ++++++ 4 files changed, 14 insertions(+), 8 deletions(-)
Title: Fuzzy Set Ordination
Description: Fuzzy set ordination is a multivariate analysis used in ecology to
relate the composition of samples to possible explanatory variables. While
differing in theory and method, in practice, the use is similar to 'constrained
ordination.' The package contains plotting and summary functions as well as
the analyses.
Author: David W. Roberts <droberts@montana.edu>
Maintainer: David W. Roberts <droberts@montana.edu>
Diff between fso versions 2.1-1 dated 2018-06-01 and 2.1-2 dated 2022-09-26
DESCRIPTION | 9 ++++----- MD5 | 16 ++++++++-------- R/fso.R | 42 +++++++++++++++++++----------------------- inst/ChangeLog | 9 ++++++++- man/fso.Rd | 3 +-- man/mfso.Rd | 2 -- man/plot.fso.Rd | 3 --- man/plot.mfso.Rd | 1 - man/step.mfso.Rd | 1 - 9 files changed, 40 insertions(+), 46 deletions(-)
Title: Computing Comorbidity Scores
Description: Computing comorbidity indices and scores such as the weighted Charlson
score (Charlson, 1987 <doi:10.1016/0021-9681(87)90171-8>) and the Elixhauser
comorbidity score (Elixhauser, 1998 <doi:10.1097/00005650-199801000-00004>)
using ICD-9-CM or ICD-10 codes (Quan, 2005 <doi:10.1097/01.mlr.0000182534.19832.83>).
Australian and Swedish modifications of the Charlson Comorbidity Index are available
as well (Sundararajan, 2004 <doi:10.1016/j.jclinepi.2004.03.012> and Ludvigsson, 2021
<doi:10.2147/CLEP.S282475>).
Author: Alessandro Gasparini [aut, cre]
,
Hojjat Salmasian [ctb] ,
Jonathan Williman [ctb] ,
Sing Yi Chia [ctb] ,
Edmund Teo [ctb]
Maintainer: Alessandro Gasparini <alessandro@ellessenne.xyz>
Diff between comorbidity versions 1.0.3 dated 2022-07-12 and 1.0.5 dated 2022-09-26
DESCRIPTION | 13 +-- MD5 | 34 ++++---- NEWS.md | 18 ++++ R/comorbidity-package.R | 7 + R/comorbidity.R | 44 +++++++--- R/score.R | 30 +++++-- R/zzz.R | 4 README.md | 6 - inst/doc/A-introduction.Rmd | 2 inst/doc/A-introduction.html | 157 ++++++++++++++++++------------------- inst/doc/B-comorbidity-scores.html | 18 ++-- man/comorbidity-package.Rd | 7 + man/comorbidity.Rd | 42 +++++++-- man/figures/hex.png |binary man/score.Rd | 32 ++++++- tests/testthat/test-#55.R | 22 ++--- tests/testthat/test-comorbidity.R | 6 - vignettes/A-introduction.Rmd | 2 18 files changed, 275 insertions(+), 169 deletions(-)
Title: Short Sprints
Description: Create short sprint (<6sec) profiles using the split times or the radar gun data.
Mono-exponential equation is used to estimate maximal sprinting speed (MSS), relative acceleration (TAU),
and other parameters such us maximal acceleration (MAC) and maximal relative power (PMAX). These parameters
can be used to predict kinematic and kinetics variables and to compare individuals. The modeling method utilized
in this package is based on the works of Chelly SM, Denis C. (2001) <doi: 10.1097/00005768-200102000-00024>,
Clark KP, Rieger RH, Bruno RF, Stearne DJ. (2017) <doi: 10.1519/JSC.0000000000002081>,
Furusawa K, Hill AV, Parkinson JL (1927) <doi: 10.1098/rspb.1927.0035>,
Greene PR. (1986) <doi: 10.1016/0025-5564(86)90063-5>, and
Samozino P. (2018) <doi: 10.1007/978-3-319-05633-3_11>.
Author: Mladen Jovanović [aut, cre],
Jason D. Vescovi [dtc]
Maintainer: Mladen Jovanović <coach.mladen.jovanovic@gmail.com>
Diff between shorts versions 2.0.0 dated 2022-07-07 and 2.1.0 dated 2022-09-26
DESCRIPTION | 8 MD5 | 47 ++-- NAMESPACE | 6 NEWS.md | 10 R/find-functions.R | 329 +++++++++++++++++++++++++++++- R/format-splits.R | 14 - R/make-FV-profile.R | 37 +++ R/model-tether.R |only R/predict-functions.R | 23 ++ R/shorts-S3.R | 2 R/shorts-constructors.R | 16 + README.md | 248 ++++++++++++++-------- inst/CITATION | 8 man/figures/README-unnamed-chunk-12-1.png |binary man/figures/README-unnamed-chunk-13-1.png |binary man/figures/README-unnamed-chunk-14-1.png |binary man/figures/README-unnamed-chunk-15-1.png |only man/figures/README-unnamed-chunk-19-1.png |binary man/figures/README-unnamed-chunk-20-1.png |binary man/figures/README-unnamed-chunk-21-1.png |binary man/figures/README-unnamed-chunk-22-1.png |only man/figures/README-unnamed-chunk-24-1.png |only man/find_functions.Rd | 104 +++++++++ man/format_splits.Rd | 1 man/make_FV_profile.Rd | 13 + man/model_tether.Rd |only man/predict_kinematics.Rd | 7 27 files changed, 743 insertions(+), 130 deletions(-)
Title: Colorful Data Frames in R Terminal
Description: Colorful Data Frames in the terminal. The new class does
change the behaviour of any of the objects, but adds a style
definition and a print method. Using ANSI escape codes, it
colors the terminal output of data frames. Some column types
(such as p-values and identifiers) are automatically
recognized.
Author: January Weiner [aut, cre]
Maintainer: January Weiner <january.weiner@gmail.com>
Diff between colorDF versions 0.1.5 dated 2022-09-25 and 0.1.7 dated 2022-09-26
DESCRIPTION | 6 +++--- MD5 | 19 ++++++++++--------- R/definitions.R |only R/print.R | 12 ++++++++++++ R/styles.R | 2 +- R/summary.R | 18 ++++++++---------- R/themes.R | 10 +++++----- inst/doc/colorDF.R | 5 ----- inst/doc/colorDF.Rmd | 29 ----------------------------- inst/doc/colorDF.html | 50 ++++++++++++++++++++------------------------------ vignettes/colorDF.Rmd | 29 ----------------------------- 11 files changed, 59 insertions(+), 121 deletions(-)
Title: Estimating Dynamic Heritability and Twin Model Comparison
Description: Twin models that are able to estimate the dynamic behaviour of the variance components in the classical twin models with respect to age using B-splines and P-splines.
Author: Liang He
Maintainer: Liang He <lianghe@health.sdu.dk>
Diff between ACEt versions 1.8.1 dated 2020-10-21 and 1.8.2 dated 2022-09-26
DESCRIPTION | 30 ++++++++++++++---------------- MD5 | 31 +++++++++++++++++++------------ NAMESPACE | 3 ++- R/acetp_mcmc.R | 15 +++++++++------ R/plot_AtCtEt.R | 3 ++- R/plot_AtCtEt_h.R | 9 ++++++--- R/plot_AtCtEtp.R | 3 ++- R/plot_acet.R | 15 ++++----------- build |only data/data_ace.rda |binary inst |only man/ACEt-package.Rd | 6 +++--- src/AtCtEt.cpp | 36 ++++++++++++------------------------ src/AtCtEtp.cpp | 48 ++++++++++++++++-------------------------------- src/AtEtp.cpp | 48 ++++++++++++++++-------------------------------- vignettes |only 16 files changed, 105 insertions(+), 142 deletions(-)
Title: 3D Visualization Using OpenGL
Description: Provides medium to high level functions for 3D interactive graphics, including
functions modelled on base graphics (plot3d(), etc.) as well as functions for
constructing representations of geometric objects (cube3d(), etc.). Output
may be on screen using OpenGL, or to various standard 3D file formats including
WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.
Author: Duncan Murdoch [aut, cre],
Daniel Adler [aut],
Oleg Nenadic [ctb],
Simon Urbanek [ctb],
Ming Chen [ctb],
Albrecht Gebhardt [ctb],
Ben Bolker [ctb],
Gabor Csardi [ctb],
Adam Strzelecki [ctb],
Alexander Senger [ctb],
The R Core Team [ctb, cph],
Dirk Ed [...truncated...]
Maintainer: Duncan Murdoch <murdoch.duncan@gmail.com>
Diff between rgl versions 0.109.6 dated 2022-07-08 and 0.110.2 dated 2022-09-26
rgl-0.109.6/rgl/inst/htmlwidgets/lib/rglClass/rglClass.min.js |only rgl-0.110.2/rgl/DESCRIPTION | 8 rgl-0.110.2/rgl/MD5 | 105 +-- rgl-0.110.2/rgl/NAMESPACE | 2 rgl-0.110.2/rgl/NEWS.md | 50 + rgl-0.110.2/rgl/R/as.mesh3d.default.R | 12 rgl-0.110.2/rgl/R/axes.R | 74 +- rgl-0.110.2/rgl/R/buffer.R | 88 ++- rgl-0.110.2/rgl/R/enum.R | 10 rgl-0.110.2/rgl/R/internal.R | 6 rgl-0.110.2/rgl/R/material.R | 25 rgl-0.110.2/rgl/R/obj.R | 20 rgl-0.110.2/rgl/R/persp3d.R | 2 rgl-0.110.2/rgl/R/plotmath3d.R | 2 rgl-0.110.2/rgl/R/r3d.rgl.R | 7 rgl-0.110.2/rgl/R/rglwidget.R | 4 rgl-0.110.2/rgl/R/scene.R | 265 ++++------ rgl-0.110.2/rgl/R/shapelist3d.R | 2 rgl-0.110.2/rgl/R/triangulate.R | 20 rgl-0.110.2/rgl/R/zzz.R | 2 rgl-0.110.2/rgl/inst/doc/WebGL.html | 91 +-- rgl-0.110.2/rgl/inst/doc/pkgdown.html | 20 rgl-0.110.2/rgl/inst/doc/rgl.Rmd | 2 rgl-0.110.2/rgl/inst/doc/rgl.html | 136 ++--- rgl-0.110.2/rgl/inst/doc/transparency.html | 27 - rgl-0.110.2/rgl/inst/htmlwidgets/lib/rglClass/draw.src.js | 29 - rgl-0.110.2/rgl/inst/htmlwidgets/lib/rglClass/init.src.js | 5 rgl-0.110.2/rgl/man/Buffer.Rd | 150 +++-- rgl-0.110.2/rgl/man/bg.Rd | 2 rgl-0.110.2/rgl/man/gltfTypes.Rd | 2 rgl-0.110.2/rgl/man/material.Rd | 38 + rgl-0.110.2/rgl/man/polygon3d.Rd | 5 rgl-0.110.2/rgl/man/rglShared.Rd | 7 rgl-0.110.2/rgl/man/rglwidget.Rd | 7 rgl-0.110.2/rgl/src/BBoxDeco.cpp | 5 rgl-0.110.2/rgl/src/Material.cpp | 18 rgl-0.110.2/rgl/src/Material.h | 1 rgl-0.110.2/rgl/src/Texture.cpp | 6 rgl-0.110.2/rgl/src/api.cpp | 41 - rgl-0.110.2/rgl/src/api.h | 2 rgl-0.110.2/rgl/src/geom.cpp | 21 rgl-0.110.2/rgl/src/gui.cpp | 3 rgl-0.110.2/rgl/src/init.cpp | 3 rgl-0.110.2/rgl/src/subscene.cpp | 8 rgl-0.110.2/rgl/src/x11gui.cpp | 5 rgl-0.110.2/rgl/tests/testthat/testdata/mergeVertices.rds |binary rgl-0.110.2/rgl/tests/testthat/testdata/obj.rds |binary rgl-0.110.2/rgl/tests/testthat/testdata/qmesh3d.rds |binary rgl-0.110.2/rgl/tests/testthat/testdata/r3d.rds |binary rgl-0.110.2/rgl/tests/testthat/testdata/shade3detc.rds |binary rgl-0.110.2/rgl/tests/testthat/testdata/subscenes.rds |binary rgl-0.110.2/rgl/tests/testthat/testdata/tmesh3d.rds |binary rgl-0.110.2/rgl/tests/testthat/testdata/transformations.rds |binary rgl-0.110.2/rgl/vignettes/rgl.Rmd | 2 54 files changed, 800 insertions(+), 540 deletions(-)
Title: Distributional Stochastic Frontier Analysis
Description: Framework to fit distributional stochastic frontier models. Casts the stochastic frontier model into the flexible framework of distributional regression or otherwise known as General Additive Models of Location, Scale and Shape (GAMLSS). Allows for linear, non-linear, random and spatial effects on all the parameters of the distribution of the output, e.g. effects on the production or cost function, heterogeneity of the noise and inefficiency. Available distributions are the normal-halfnormal and normal-exponential distribution. Estimation via the fast and reliable routines of the 'mgcv' package. For more details see Schmidt R, Kneib T (2022) <doi:10.48550/arXiv.2208.10294>.
Author: Rouven Schmidt [aut, cre]
Maintainer: Rouven Schmidt <rouven.schmidt@tu-clausthal.de>
Diff between dsfa versions 0.0.3 dated 2022-09-07 and 1.0.0 dated 2022-09-26
dsfa-0.0.3/dsfa/R/cop_utility.R |only dsfa-0.0.3/dsfa/man/dcop_copula.Rd |only dsfa-0.0.3/dsfa/man/erfcinv.Rd |only dsfa-1.0.0/dsfa/DESCRIPTION | 8 dsfa-1.0.0/dsfa/MD5 | 77 +- dsfa-1.0.0/dsfa/NAMESPACE | 8 dsfa-1.0.0/dsfa/NEWS.md |only dsfa-1.0.0/dsfa/R/OwenT.R |only dsfa-1.0.0/dsfa/R/chainrule.R | 62 +- dsfa-1.0.0/dsfa/R/comperr.R | 68 +- dsfa-1.0.0/dsfa/R/comperr_mv.R | 121 ++-- dsfa-1.0.0/dsfa/R/comperr_mv_mgcv.R | 134 +++-- dsfa-1.0.0/dsfa/R/cop.R | 907 +++++++++++++++++++++------------- dsfa-1.0.0/dsfa/R/cop_mgcv.R | 195 +++++-- dsfa-1.0.0/dsfa/R/dsfa.R | 95 ++- dsfa-1.0.0/dsfa/R/efficiency.R | 2 dsfa-1.0.0/dsfa/R/elasticity.R | 2 dsfa-1.0.0/dsfa/R/erf.R |only dsfa-1.0.0/dsfa/R/normexp.R | 18 dsfa-1.0.0/dsfa/R/normexp_mgcv.R | 13 dsfa-1.0.0/dsfa/R/normhnorm.R | 56 -- dsfa-1.0.0/dsfa/R/normhnorm_mgcv.R | 13 dsfa-1.0.0/dsfa/R/reparametrize.R | 24 dsfa-1.0.0/dsfa/R/utility_functions.R | 89 --- dsfa-1.0.0/dsfa/R/zeta.R |only dsfa-1.0.0/dsfa/build/partial.rdb |binary dsfa-1.0.0/dsfa/inst/REFERENCES.bib | 21 dsfa-1.0.0/dsfa/man/OwenT.Rd |only dsfa-1.0.0/dsfa/man/chainrule.Rd | 4 dsfa-1.0.0/dsfa/man/comperr_mv.Rd | 29 - dsfa-1.0.0/dsfa/man/cop.Rd | 47 + dsfa-1.0.0/dsfa/man/dcomperr.Rd | 31 - dsfa-1.0.0/dsfa/man/dcomperr_mv.Rd | 84 +-- dsfa-1.0.0/dsfa/man/dcop.Rd | 66 +- dsfa-1.0.0/dsfa/man/dnormexp.Rd | 6 dsfa-1.0.0/dsfa/man/dnormhnorm.Rd | 10 dsfa-1.0.0/dsfa/man/dsfa.Rd | 92 ++- dsfa-1.0.0/dsfa/man/efficiency.Rd | 2 dsfa-1.0.0/dsfa/man/elasticity.Rd | 2 dsfa-1.0.0/dsfa/man/erf.Rd |only dsfa-1.0.0/dsfa/man/normexp.Rd | 9 dsfa-1.0.0/dsfa/man/normhnorm.Rd | 9 dsfa-1.0.0/dsfa/man/pos_eigen.Rd |only dsfa-1.0.0/dsfa/man/reparametrize.Rd | 12 dsfa-1.0.0/dsfa/man/zeta.Rd |only 45 files changed, 1374 insertions(+), 942 deletions(-)
Title: Exhaustive Chemical Enumeration for United Formula Annotation
Description: A pipeline to annotate a number of peaks from the IDSL.IPA peaklists using an exhaustive chemical enumeration-based approach. This package can perform elemental composition calculations using the following 15 elements : C, B, Br, Cl, K, S, Se, Si, N, H, As, F, I, Na, O, and P.
Author: Sadjad Fakouri-Baygi [cre, aut]
,
Dinesh Barupal [aut]
Maintainer: Sadjad Fakouri-Baygi <sadjad.fakouri-baygi@mssm.edu>
Diff between IDSL.UFAx versions 1.5 dated 2022-09-09 and 1.6 dated 2022-09-26
DESCRIPTION | 6 ++-- MD5 | 9 +++--- R/UFAx_score_coefficient_corrector.R | 46 +++++++++++++++++++++-------------- inst/CITATION |only inst/extdata/UFAx_parameters.xlsx |binary man/UFAx_workflow.Rd | 7 ++--- 6 files changed, 39 insertions(+), 29 deletions(-)
Title: Plot Data on Oceanographic Maps using 'ggplot2'
Description: Allows plotting data on bathymetric maps using 'ggplot2'. Plotting
oceanographic spatial data is made as simple as feasible, but also flexible
for custom modifications. Data that contain geographic information from
anywhere around the globe can be plotted on maps generated by the basemap()
or qmap() functions using 'ggplot2' layers separated by the '+' operator. The
package uses spatial shapefiles stored in the 'ggOceanMapsData' package,
geospatial packages for R to manipulate, and the 'ggspatial' package to help
to plot these shapefiles. High-resolution shapefiles for detailed maps are
stored on GitHub and downloaded automatically when needed.
Author: Mikko Vihtakari [aut, cre] ,
Yves Reecht [ctb] ,
Hadley Wickham [ctb],
Simon O'Hanlon [ctb],
Roger Bivand [ctb]
Maintainer: Mikko Vihtakari <mikko.vihtakari@hi.no>
Diff between ggOceanMaps versions 1.3.0 dated 2022-09-20 and 1.3.4 dated 2022-09-26
DESCRIPTION | 8 ++++---- MD5 | 30 +++++++++++++++--------------- R/basemap.R | 21 +++++++++++---------- R/basemap_data.R | 15 ++++++++++++--- R/datasets-docs.R | 6 ++++++ R/dist2land.R | 3 +++ R/qmap.R | 6 ++---- R/reorder_layers.R | 2 ++ R/shapefile_list.R | 8 ++++++++ man/basemap.Rd | 19 +++++++++---------- man/dist2land.Rd | 3 +++ man/fdir_main_areas.Rd | 2 ++ man/fdir_sub_areas.Rd | 2 ++ man/ices_areas.Rd | 2 ++ man/qmap.Rd | 6 ++---- man/reorder_layers.Rd | 2 ++ 16 files changed, 85 insertions(+), 50 deletions(-)
Title: High Dimensional Numerical and Symbolic Calculus
Description: Efficient C++ optimized functions for numerical and symbolic calculus as described in Guidotti (2022) <doi:10.18637/jss.v104.i05>. It includes basic arithmetic, tensor calculus, Einstein summing convention, fast computation of the Levi-Civita symbol and generalized Kronecker delta, Taylor series expansion, multivariate Hermite polynomials, high-order derivatives, ordinary differential equations, differential operators (Gradient, Jacobian, Hessian, Divergence, Curl, Laplacian) and numerical integration in arbitrary orthogonal coordinate systems: cartesian, polar, spherical, cylindrical, parabolic or user defined by custom scale factors.
Author: Emanuele Guidotti [aut, cre]
Maintainer: Emanuele Guidotti <emanuele.guidotti@unine.ch>
Diff between calculus versions 0.3.4 dated 2022-08-20 and 1.0.0 dated 2022-09-26
DESCRIPTION | 8 - MD5 | 155 +++++++++++++++++------------------ NEWS.md | 4 R/contraction.R | 2 R/delta.R | 2 R/derivative.R | 2 R/einstein.R | 2 R/epsilon.R | 2 R/evaluate.R | 2 R/hermite.R | 2 R/integral.R | 2 R/mxdet.R | 2 R/mxinv.R | 2 R/mxtr.R | 2 R/ode.R | 2 R/operators.R | 32 +++---- R/partitions.R | 2 R/taylor.R | 2 R/utils.R | 10 +- README.md | 21 ++-- build/partial.rdb |only inst/CITATION | 23 ++--- inst/doc/derivatives.Rmd | 21 ++-- inst/doc/derivatives.html | 24 ++--- inst/doc/differential-operators.Rmd | 21 ++-- inst/doc/differential-operators.html | 24 ++--- inst/doc/einstein.Rmd | 21 ++-- inst/doc/einstein.html | 24 ++--- inst/doc/hermite.Rmd | 21 ++-- inst/doc/hermite.html | 24 ++--- inst/doc/integrals.Rmd | 24 ++--- inst/doc/integrals.html | 24 ++--- inst/doc/ode.Rmd | 22 ++-- inst/doc/ode.html | 24 ++--- inst/doc/taylor.Rmd | 21 ++-- inst/doc/taylor.html | 24 ++--- man/c2e.Rd | 2 man/calculus-package.Rd | 2 man/contraction.Rd | 2 man/cross.Rd | 2 man/curl.Rd | 2 man/delta.Rd | 2 man/derivative.Rd | 2 man/diagonal.Rd | 2 man/divergence.Rd | 2 man/e2c.Rd | 2 man/einstein.Rd | 2 man/epsilon.Rd | 2 man/evaluate.Rd | 2 man/gradient.Rd | 2 man/grapes-diff-grapes.Rd | 2 man/grapes-div-grapes.Rd | 2 man/grapes-dot-grapes.Rd | 2 man/grapes-inner-grapes.Rd | 2 man/grapes-kronecker-grapes.Rd | 2 man/grapes-outer-grapes.Rd | 2 man/grapes-prod-grapes.Rd | 2 man/grapes-sum-grapes.Rd | 2 man/hermite.Rd | 2 man/hessian.Rd | 2 man/index.Rd | 2 man/integral.Rd | 2 man/jacobian.Rd | 2 man/laplacian.Rd | 2 man/mx.Rd | 2 man/mxdet.Rd | 2 man/mxinv.Rd | 2 man/mxtr.Rd | 2 man/ode.Rd | 2 man/partitions.Rd | 2 man/taylor.Rd | 2 man/wrap.Rd | 2 vignettes/derivatives.Rmd | 21 ++-- vignettes/differential-operators.Rmd | 21 ++-- vignettes/einstein.Rmd | 21 ++-- vignettes/hermite.Rmd | 21 ++-- vignettes/integrals.Rmd | 24 ++--- vignettes/ode.Rmd | 22 ++-- vignettes/taylor.Rmd | 21 ++-- 79 files changed, 425 insertions(+), 398 deletions(-)
Title: A Tidy Tool for Phylogenetic Tree Data Manipulation
Description: Phylogenetic tree generally contains multiple components including node, edge, branch and associated data. 'tidytree' provides an approach to convert tree object to tidy data frame as well as provides tidy interfaces to manipulate tree data.
Author: Guangchuang Yu [aut, cre, cph]
,
Bradley Jones [ctb],
Zebulun Arendsee [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between tidytree versions 0.4.0 dated 2022-08-13 and 0.4.1 dated 2022-09-26
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/zzz.R | 7 +++++-- inst/CITATION | 6 ++++-- inst/doc/tidytree.html | 4 ++-- 6 files changed, 23 insertions(+), 14 deletions(-)
Title: Identify Rogue Taxa in Sets of Phylogenetic Trees
Description: Rogue ("wildcard") taxa are leaves with uncertain phylogenetic
position.
Their position may vary from tree to tree under inference methods that yield a
tree set (e.g. bootstrapping, Bayesian tree searches, maximum parsimony).
The presence of rogue taxa in a tree set can potentially remove all
information from a consensus tree. The information content of a consensus
tree - a function of its resolution and branch support values - can often be
increased by removing rogue taxa.
'Rogue' provides an explicitly information-theoretic approach to rogue
detection (Smith 2022) <doi:10.1093/sysbio/syab099>,
and an interface to 'RogueNaRok' (Aberer et al. 2013)
<doi:10.1093/sysbio/sys078>.
Author: Martin R. Smith [aut, cre, cph]
,
Andre J. Aberer [aut, cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between Rogue versions 2.1.2 dated 2022-08-16 and 2.1.3 dated 2022-09-26
DESCRIPTION | 6 ++--- MD5 | 34 ++++++++++++++-------------- NEWS.md | 6 +++++ R/Rogue-package.R | 4 +-- R/stability.R | 35 ++++++++++++++++------------- R/utilities.R | 2 - R/zz_RogueNaRok.R | 20 ++++++++-------- R/zzz.R | 12 ---------- build/partial.rdb |binary inst/doc/Bayesian.html | 4 +-- man/Rogue-package.Rd | 4 +-- man/RogueTaxa.Rd | 10 ++++---- man/TipInstability.Rd | 23 +++++++++++++++---- man/TipVolatility.Rd | 6 ++--- tests/testthat.R | 4 +-- tests/testthat/test-RogueNaRok.R | 24 ++++++++++---------- tests/testthat/test-RogueTaxa.R | 46 +++++++++++++++++++-------------------- tests/testthat/test-stability.R | 10 ++++---- 18 files changed, 131 insertions(+), 119 deletions(-)
Title: The Multivariate Normal and t Distributions, and Their Truncated
Versions
Description: Functions are provided for computing the density and the
distribution function of d-dimensional normal and "t" random variables,
possibly truncated (on one side or two sides), and for generating random
vectors sampled from these distributions, except sampling from the truncated
"t". Moments of arbitrary order of a multivariate truncated normal are
computed, and converted to cumulants up to order 4.
Probabilities are computed via non-Monte Carlo methods; different routines
are used in the case d=1, d=2, d=3, d>3, if d denotes the dimensionality.
Author: Adelchi Azzalini [aut, cre],
Alan Genz [aut] ,
Alan Miller [ctb] ,
Michael J. Wichura [ctb] ,
G. W. Hill [ctb] ,
Yihong Ge [ctb] .
Maintainer: Adelchi Azzalini <adelchi.azzalini@unipd.it>
Diff between mnormt versions 2.1.0 dated 2022-06-07 and 2.1.1 dated 2022-09-26
mnormt-2.1.0/mnormt/NEWS |only mnormt-2.1.1/mnormt/DESCRIPTION | 8 +++---- mnormt-2.1.1/mnormt/INDEX |only mnormt-2.1.1/mnormt/MD5 | 21 +++++++++--------- mnormt-2.1.1/mnormt/R/mnormt.R | 34 +++++++++++++++++++----------- mnormt-2.1.1/mnormt/R/truncNorm.R | 9 ++++--- mnormt-2.1.1/mnormt/build/partial.rdb |binary mnormt-2.1.1/mnormt/inst/NEWS.Rd |only mnormt-2.1.1/mnormt/man/mnorm.Rd | 28 ++++++++++++++---------- mnormt-2.1.1/mnormt/man/mom.mtruncnorm.Rd | 25 +++++++++++++--------- mnormt-2.1.1/mnormt/man/mt.Rd | 28 +++++++++++++----------- mnormt-2.1.1/mnormt/man/mtruncnorm.Rd | 23 +++++++++++--------- mnormt-2.1.1/mnormt/man/recintab.Rd | 3 ++ 13 files changed, 104 insertions(+), 75 deletions(-)
Title: Intensity Analysis of Spatial Point Patterns on Complex Networks
Description: Tools to analyze point patterns in space occurring over planar network structures derived from graph-related intensity measures for undirected, directed, and mixed networks.
This package is based on the following research: Eckardt and Mateu (2018) <doi:10.1080/10618600.2017.1391695>. Eckardt and Mateu (2021) <doi:10.1007/s11749-020-00720-4>.
Author: Pol Llagostera [aut, cre],
Matthias Eckardt [aut]
Maintainer: Pol Llagostera <pol.llagostera@udl.cat>
Diff between intensitynet versions 1.3.0 dated 2022-05-16 and 1.3.1 dated 2022-09-26
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- NEWS.md | 4 ++++ 3 files changed, 11 insertions(+), 7 deletions(-)
Title: Interface to the 'CDK' Libraries
Description: Allows the user to access functionality in the
'CDK', a Java framework for chemoinformatics. This allows the user to load
molecules, evaluate fingerprints, calculate molecular descriptors and so on.
In addition, the 'CDK' API allows the user to view structures in 2D.
Author: Rajarshi Guha [aut, cph],
Zachary Charlop-Powers [cre],
Emma Schymanski [ctb]
Maintainer: Zachary Charlop-Powers <zach.charlop.powers@gmail.com>
Diff between rcdk versions 3.6.0 dated 2021-10-17 and 3.7.0 dated 2022-09-26
rcdk-3.6.0/rcdk/NEWS |only rcdk-3.7.0/rcdk/DESCRIPTION | 12 rcdk-3.7.0/rcdk/MD5 | 63 +- rcdk-3.7.0/rcdk/NEWS.md |only rcdk-3.7.0/rcdk/R/atoms.R | 66 +- rcdk-3.7.0/rcdk/R/desc.R | 2 rcdk-3.7.0/rcdk/R/formula.R | 10 rcdk-3.7.0/rcdk/R/io.R | 27 rcdk-3.7.0/rcdk/R/props.R | 7 rcdk-3.7.0/rcdk/R/smsd.R | 2 rcdk-3.7.0/rcdk/R/visual.R | 8 rcdk-3.7.0/rcdk/build/vignette.rds |binary rcdk-3.7.0/rcdk/inst/cont/rcdk.jar |binary rcdk-3.7.0/rcdk/inst/doc/molform.html | 431 ++++++++++++--- rcdk-3.7.0/rcdk/inst/doc/using-rcdk.Rmd | 6 rcdk-3.7.0/rcdk/inst/doc/using-rcdk.html | 706 ++++++++++++++++++++----- rcdk-3.7.0/rcdk/inst/unitTests/runit.formula.R |only rcdk-3.7.0/rcdk/inst/unitTests/runit.rcdk.R | 2 rcdk-3.7.0/rcdk/man/Atoms.Rd | 2 rcdk-3.7.0/rcdk/man/get.atom.index.Rd | 8 rcdk-3.7.0/rcdk/man/get.atomic.number.Rd | 2 rcdk-3.7.0/rcdk/man/get.charge.Rd | 8 rcdk-3.7.0/rcdk/man/get.connected.atoms.Rd | 7 rcdk-3.7.0/rcdk/man/get.formal.charge.Rd | 7 rcdk-3.7.0/rcdk/man/get.hydrogen.count.Rd | 9 rcdk-3.7.0/rcdk/man/get.point2d.Rd | 9 rcdk-3.7.0/rcdk/man/get.point3d.Rd | 9 rcdk-3.7.0/rcdk/man/get.properties.Rd | 2 rcdk-3.7.0/rcdk/man/get.symbol.Rd | 6 rcdk-3.7.0/rcdk/man/is.aliphatic.Rd | 8 rcdk-3.7.0/rcdk/man/is.aromatic.Rd | 8 rcdk-3.7.0/rcdk/man/is.in.ring.Rd | 8 rcdk-3.7.0/rcdk/man/set.atom.types.Rd | 10 rcdk-3.7.0/rcdk/vignettes/using-rcdk.Rmd | 6 34 files changed, 1066 insertions(+), 385 deletions(-)
Title: Hidden Markov Models with Discrete Non-Parametric Observation
Distributions
Description: Fits hidden Markov models with discrete non-parametric
observation distributions to data sets. The observations may
be univariate or bivariate. Simulates data from such models.
Finds most probable underlying hidden states, the most
probable sequences of such states, and the log likelihood
of a collection of observations given the parameters of
the model. Auxiliary predictors are accommodated in the
univariate setting.
Author: Rolf Turner
Maintainer: Rolf Turner <r.turner@auckland.ac.nz>
Diff between hmm.discnp versions 3.0-7 dated 2022-02-08 and 3.0-9 dated 2022-09-26
hmm.discnp-3.0-7/hmm.discnp/R/fix.tpm.R |only hmm.discnp-3.0-9/hmm.discnp/ChangeLog | 44 ++ hmm.discnp-3.0-9/hmm.discnp/DESCRIPTION | 8 hmm.discnp-3.0-9/hmm.discnp/MD5 | 80 ++-- hmm.discnp-3.0-9/hmm.discnp/R/First.R | 14 hmm.discnp-3.0-9/hmm.discnp/R/checkStartVal.R | 13 hmm.discnp-3.0-9/hmm.discnp/R/ffun.R | 24 - hmm.discnp-3.0-9/hmm.discnp/R/hmmLM.R | 3 hmm.discnp-3.0-9/hmm.discnp/R/hmmNumOpt.R | 7 hmm.discnp-3.0-9/hmm.discnp/R/hmmSD.R | 3 hmm.discnp-3.0-9/hmm.discnp/R/hmmUV.R | 20 - hmm.discnp-3.0-9/hmm.discnp/R/lmstep.R | 2 hmm.discnp-3.0-9/hmm.discnp/R/makeDat.R | 2 hmm.discnp-3.0-9/hmm.discnp/R/revise.rho.R | 4 hmm.discnp-3.0-9/hmm.discnp/R/steepest.R | 21 - hmm.discnp-3.0-9/hmm.discnp/R/suffices.R |only hmm.discnp-3.0-9/hmm.discnp/data/Bovine.rda |binary hmm.discnp-3.0-9/hmm.discnp/data/Cryptosporidiosis.rda |binary hmm.discnp-3.0-9/hmm.discnp/data/Downloads.rda |binary hmm.discnp-3.0-9/hmm.discnp/data/EricssonB_Jul2.rda |binary hmm.discnp-3.0-9/hmm.discnp/data/FattyLiver.rda |binary hmm.discnp-3.0-9/hmm.discnp/data/FattyLiver2.rda |binary hmm.discnp-3.0-9/hmm.discnp/data/Hanta.rda |binary hmm.discnp-3.0-9/hmm.discnp/data/IPs.rda |binary hmm.discnp-3.0-9/hmm.discnp/data/InfantEEGsleepstates.rda |binary hmm.discnp-3.0-9/hmm.discnp/data/LegionnairesDisease.rda |binary hmm.discnp-3.0-9/hmm.discnp/data/OffshoreRigcountsAlaska.rda |binary hmm.discnp-3.0-9/hmm.discnp/data/PriceStability.rda |binary hmm.discnp-3.0-9/hmm.discnp/data/Strikes.rda |binary hmm.discnp-3.0-9/hmm.discnp/data/SydColDisc.rda |binary hmm.discnp-3.0-9/hmm.discnp/data/WoodPeweeSong.rda |binary hmm.discnp-3.0-9/hmm.discnp/data/ccprSim.rda |binary hmm.discnp-3.0-9/hmm.discnp/data/ftLiardFlows.rda |binary hmm.discnp-3.0-9/hmm.discnp/data/goldparticle380.rda |binary hmm.discnp-3.0-9/hmm.discnp/data/lesionCount.rda |binary hmm.discnp-3.0-9/hmm.discnp/data/linLandFlows.rda |binary hmm.discnp-3.0-9/hmm.discnp/data/portMannFlows.rda |binary hmm.discnp-3.0-9/hmm.discnp/data/portMannSedCon.rda |binary hmm.discnp-3.0-9/hmm.discnp/data/portMannSedLoads.rda |binary hmm.discnp-3.0-9/hmm.discnp/man/hmm.Rd | 196 +++++++++-- hmm.discnp-3.0-9/hmm.discnp/man/hmm.discnp-internal.Rd | 6 hmm.discnp-3.0-9/hmm.discnp/man/viterbi.Rd | 7 42 files changed, 341 insertions(+), 113 deletions(-)
Title: Histogram-Valued Data Analysis
Description: In the framework of Symbolic Data Analysis, a relatively new
approach to the statistical analysis of multi-valued data, we consider
histogram-valued data, i.e., data described by univariate histograms. The
methods and the basic statistics for histogram-valued data are mainly based
on the L2 Wasserstein metric between distributions, i.e., the Euclidean metric
between quantile functions. The package contains unsupervised classification
techniques, least square regression and tools for histogram-valued data and for
histogram time series. An introducing paper is Irpino A. Verde R. (2015) <doi: 10.1007/s11634-014-0176-4>.
Author: Antonio Irpino [aut, cre]
Maintainer: Antonio Irpino <antonio.irpino@unicampania.it>
Diff between HistDAWass versions 1.0.6 dated 2021-06-22 and 1.0.7 dated 2022-09-26
DESCRIPTION | 12 - MD5 | 178 +++++++++---------- R/Plotting_with_ggplot.R | 2 README.md | 27 +- build/partial.rdb |binary data/HData.RData |binary man/Age_Pyramids_2014.Rd | 44 ++-- man/Agronomique.Rd | 46 ++-- man/BLOOD.Rd | 40 ++-- man/BloodBRITO.Rd | 42 ++-- man/Center.cell.MatH-methods.Rd | 50 ++--- man/DouglasPeucker.Rd | 44 ++-- man/HTS-class.Rd | 42 ++-- man/HTS.exponential.smoothing.Rd | 66 +++---- man/HTS.moving.averages.Rd | 74 +++---- man/HTS.predict.knn.Rd | 80 ++++---- man/HistDAWass-package.Rd | 120 ++++++------ man/MatH-class.Rd | 190 ++++++++++---------- man/OzoneFull.Rd | 42 ++-- man/OzoneH.Rd | 42 ++-- man/ShortestDistance.Rd | 44 ++-- man/TMatH-class.Rd | 60 +++--- man/TdistributionH-class.Rd | 78 ++++---- man/WH.1d.PCA.Rd | 132 +++++++------- man/WH.MultiplePCA.Rd | 64 +++--- man/WH.SSQ-methods.Rd | 68 +++---- man/WH.SSQ2-methods.Rd | 78 ++++---- man/WH.bind-methods.Rd | 76 ++++---- man/WH.bind.col-methods.Rd | 56 +++--- man/WH.bind.row-methods.Rd | 56 +++--- man/WH.correlation-methods.Rd | 80 ++++---- man/WH.correlation2-methods.Rd | 78 ++++---- man/WH.mat.prod-methods.Rd | 74 +++---- man/WH.mat.sum-methods.Rd | 62 +++--- man/WH.plot_multiple_Spanish.funs.Rd | 94 +++++----- man/WH.plot_multiple_indivs.Rd | 140 +++++++-------- man/WH.regression.GOF.Rd | 66 +++---- man/WH.regression.two.components.Rd | 94 +++++----- man/WH.regression.two.components.predict.Rd | 62 +++--- man/WH.var.covar-methods.Rd | 80 ++++---- man/WH.var.covar2-methods.Rd | 78 ++++---- man/WH.vec.mean-methods.Rd | 66 +++---- man/WH.vec.sum-methods.Rd | 68 +++---- man/WH_2d_Adaptive_Kohonen_maps.Rd | 260 ++++++++++++++-------------- man/WH_2d_Kohonen_maps.Rd | 202 ++++++++++----------- man/WH_MAT_DIST.Rd | 64 +++--- man/WH_adaptive.kmeans.Rd | 172 +++++++++--------- man/WH_adaptive_fcmeans.Rd | 130 +++++++------- man/WH_fcmeans.Rd | 104 +++++------ man/WH_hclust.Rd | 108 +++++------ man/WH_kmeans.Rd | 136 +++++++------- man/WassSqDistH-methods.Rd | 92 ++++----- man/checkEmptyBins-methods.Rd | 68 +++---- man/compP-methods.Rd | 62 +++--- man/compQ-methods.Rd | 76 ++++---- man/crwtransform-methods.Rd | 82 ++++---- man/data2hist.Rd | 110 +++++------ man/distributionH-class.Rd | 172 +++++++++--------- man/dotpW-methods.Rd | 116 ++++++------ man/extract-methods.Rd | 62 +++--- man/get.MatH.main.info-methods.Rd | 64 +++--- man/get.MatH.stats-methods.Rd | 116 ++++++------ man/get.MatH.varnames-methods.Rd | 40 ++-- man/get.cell.MatH-methods.Rd | 56 +++--- man/get.distr-methods.Rd | 48 ++--- man/get.histo-methods.Rd | 48 ++--- man/get.m-methods.Rd | 48 ++--- man/get.s-methods.Rd | 48 ++--- man/is.registeredMH-methods.Rd | 106 +++++------ man/kurtH-methods.Rd | 64 +++--- man/meanH-methods.Rd | 62 +++--- man/minus.Rd | 60 +++--- man/plot-HTS.Rd | 74 +++---- man/plot-MatH.Rd | 72 +++---- man/plot-TdistributionH.Rd | 50 ++--- man/plot-distributionH.Rd | 74 +++---- man/plotPredVsObs.Rd | 80 ++++---- man/plot_errors.Rd | 78 ++++---- man/plus-methods.Rd | 62 +++--- man/rQQ-methods.Rd | 80 ++++---- man/register-methods.Rd | 118 ++++++------ man/registerMH-methods.Rd | 146 +++++++-------- man/set.cell.MatH-methods.Rd | 62 +++--- man/show-MatH-methods.Rd | 44 ++-- man/show-distributionH-methods.Rd | 46 ++-- man/skewH-methods.Rd | 62 +++--- man/stdH-methods.Rd | 64 +++--- man/subsetHTS-methods.Rd | 54 ++--- man/times-methods.Rd | 54 ++--- src/RcppExports.cpp | 5 90 files changed, 3454 insertions(+), 3442 deletions(-)
Title: Bayesian Exponential Random Graph Models
Description: Bayesian analysis for exponential random graph models using advanced computational algorithms. More information can be found at: <https://acaimo.github.io/Bergm/>.
Author: Alberto Caimo [aut, cre],
Lampros Bouranis [aut],
Robert Krause [aut]
Nial Friel [ctb]
Maintainer: Alberto Caimo <alberto.caimo@tudublin.ie>
Diff between Bergm versions 5.0.4 dated 2022-08-15 and 5.0.5 dated 2022-09-26
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- inst/CITATION | 53 +++++++++++++++++++++++++++++++++++------------------ 3 files changed, 41 insertions(+), 24 deletions(-)
Title: Multiple Imputation with Automated Machine Learning
Description: Machine learning algorithms have been used for performing
single missing data imputation and most recently, multiple imputations.
However, this is the first attempt for using automated machine learning algorithms
for performing both
single and multiple imputation. Automated machine learning is a procedure for
fine-tuning the model automatic, performing a random search for a model that
results in less error, without overfitting the data. The main idea is
to allow the model to set its own parameters for imputing each variable seperately
instead of setting fixed predefined parameters to impute all variables
of the dataset.
Using automated machine learning, the package fine-tunes an Elastic
Net (default) or Gradient Boosting, Random Forest, Deep Learning, Extreme Gradient Boosting,
or Stacked Ensemble machine learning model (from one or a combination of other
supported algorithms) for imputing the missing
observations. This procedure has been implemented for the
first time by this package [...truncated...]
Author: E. F. Haghish [aut, cre, cph]
Maintainer: E. F. Haghish <haghish@uio.no>
Diff between mlim versions 0.0.9 dated 2022-09-07 and 0.2.0 dated 2022-09-26
DESCRIPTION | 38 LICENSE | 4 MD5 | 101 +- NAMESPACE | 70 - R/addNA.R | 44 - R/algoSelector.R | 144 +-- R/bootstrapWeight.R |only R/charity.R | 30 R/checkNconvert.R | 266 +++--- R/extractMetrics.R | 108 +- R/getDigits.R | 27 R/getMetrics.R | 48 - R/h2o.check.R | 78 - R/init.R | 115 +- R/is.imbalanced.R | 52 - R/is.valid.R | 52 - R/iterate.R | 1251 ++++++++++++++++++----------- R/iterationNextVar.R |only R/iteration_loop.R | 544 +++++++----- R/javaServer.R |only R/manifest.R | 200 ++-- R/matching.R | 88 +- R/meanmode.R | 70 - R/miss_per_class_error.R | 80 - R/missclass.R | 40 R/missrank.R | 48 - R/mlim.R | 1280 +++++++++++++++--------------- R/mlim.error.R | 408 ++++----- R/mlim.mids.R | 94 +- R/mlim.na.R | 154 +-- R/mlim.postimpute.R | 152 +-- R/mlim.preimpute.R | 124 +- R/mlim.summarize.R | 156 +-- R/normalize.R | 20 R/nrmse.R | 48 - R/selectVariables.R | 112 +- R/server.check.R | 78 - R/stoppingCriteria.R | 253 ++--- R/syntaxProcessing.R | 188 ++-- R/threeDots.R | 32 R/zzz.R | 16 README.md | 376 ++++---- man/charity.Rd | 52 - man/figures/flowchart_base.drawio |only man/figures/flowchart_base.png |only man/figures/flowchart_optimization.drawio |only man/figures/flowchart_optimization.png |only man/figures/procedure5.drawio |only man/figures/procedure5.png |only man/manifest.Rd | 190 ++-- man/mlim.Rd | 496 ++++++----- man/mlim.error.Rd | 174 ++-- man/mlim.mids.Rd | 88 +- man/mlim.na.Rd | 126 +- man/mlim.preimpute.Rd | 92 +- man/mlim.summarize.Rd | 72 - 56 files changed, 4415 insertions(+), 3864 deletions(-)
Title: Generate Activity Counts from Raw Accelerometer Data
Description: A tool to obtain activity counts, originally a translation of the
'python' package 'agcounts' <https://github.com/actigraph/agcounts>. This tool
allows the processing of data from any accelerometer brand, with a more flexible
approach to handle different sampling frequencies.
Author: Jairo Hidalgo Migueles
Maintainer: Jairo Hidalgo Migueles <jairo.hidalgo.migueles@gmail.com>
Diff between actilifecounts versions 1.0.0 dated 2022-05-30 and 1.1.0 dated 2022-09-26
actilifecounts-1.0.0/actilifecounts/NEWS.md |only actilifecounts-1.1.0/actilifecounts/DESCRIPTION | 13 +++---- actilifecounts-1.1.0/actilifecounts/MD5 | 18 +++++----- actilifecounts-1.1.0/actilifecounts/R/bpf_filter.R | 5 +- actilifecounts-1.1.0/actilifecounts/R/get_counts.R | 7 ++- actilifecounts-1.1.0/actilifecounts/R/resample_30hz.R | 3 + actilifecounts-1.1.0/actilifecounts/README.md | 9 +++-- actilifecounts-1.1.0/actilifecounts/inst/NEWS.Rd |only actilifecounts-1.1.0/actilifecounts/man/get_counts.Rd | 4 +- actilifecounts-1.1.0/actilifecounts/tests/testthat/test-get_counts.R | 6 +-- actilifecounts-1.1.0/actilifecounts/tests/testthat/test-pipeline.R | 6 +++ 11 files changed, 43 insertions(+), 28 deletions(-)
More information about actilifecounts at CRAN
Permanent link
Title: Modeling Workflows
Description: Managing both a 'parsnip' model and a preprocessor, such as a
model formula or recipe from 'recipes', can often be challenging. The
goal of 'workflows' is to streamline this process by bundling the
model alongside the preprocessor, all within the same object.
Author: Davis Vaughan [aut],
Simon Couch [aut, cre] ,
RStudio [cph, fnd]
Maintainer: Simon Couch <simonpatrickcouch@gmail.com>
Diff between workflows versions 1.0.0 dated 2022-07-05 and 1.1.0 dated 2022-09-26
DESCRIPTION | 17 +++++---- MD5 | 30 ++++++++-------- NEWS.md | 22 +++++++++++ R/broom.R | 17 +++++++++ R/butcher.R | 9 ++++ R/fit-action-model.R | 14 +++++++ R/pre-action-formula.R | 22 +++++++++++ inst/doc/stages.html | 14 +++---- man/workflows-package.Rd | 7 +++ tests/testthat/_snaps/fit-action-model.md | 9 ++++ tests/testthat/_snaps/pre-action-formula.md | 9 ++++ tests/testthat/test-broom.R | 52 ++++++++++++++++++++++++++++ tests/testthat/test-butcher.R | 27 ++++++++++++++ tests/testthat/test-fit-action-model.R | 30 ++++++++++++++++ tests/testthat/test-pre-action-formula.R | 19 ++++++++++ vignettes/extras/getting-started.Rmd | 26 ++++++-------- 16 files changed, 280 insertions(+), 44 deletions(-)
Title: Risk Regression Models and Prediction Scores for Survival
Analysis with Competing Risks
Description: Implementation of the following methods for event history analysis.
Risk regression models for survival endpoints also in the presence of competing
risks are fitted using binomial regression based on a time sequence of binary
event status variables. A formula interface for the Fine-Gray regression model
and an interface for the combination of cause-specific Cox regression models.
A toolbox for assessing and comparing performance of risk predictions (risk
markers and risk prediction models). Prediction performance is measured by the
Brier score and the area under the ROC curve for binary possibly time-dependent
outcome. Inverse probability of censoring weighting and pseudo values are used
to deal with right censored data. Lists of risk markers and lists of risk models
are assessed simultaneously. Cross-validation repeatedly splits the data, trains
the risk prediction models on one part of each split and then summarizes and
compares the performance across splits.
Author: Thomas Alexander Gerds [aut, cre],
Johan Sebastian Ohlendorff [aut],
Paul Blanche [ctb],
Rikke Mortensen [ctb],
Marvin Wright [ctb],
Nikolaj Tollenaar [ctb],
John Muschelli [ctb],
Ulla Brasch Mogensen [ctb],
Brice Ozenne [aut]
Maintainer: Thomas Alexander Gerds <tag@biostat.ku.dk>
Diff between riskRegression versions 2022.09.13 dated 2022-09-17 and 2022.09.23 dated 2022-09-26
riskRegression-2022.09.13/riskRegression/src/getInfluenceFunctionBrierCVCensoringKM.cpp |only riskRegression-2022.09.23/riskRegression/DESCRIPTION | 6 riskRegression-2022.09.23/riskRegression/MD5 | 37 riskRegression-2022.09.23/riskRegression/R/AUC.competing.risks.R | 98 riskRegression-2022.09.23/riskRegression/R/AUC.survival.R | 26 riskRegression-2022.09.23/riskRegression/R/Brier.competing.risks.R | 59 riskRegression-2022.09.23/riskRegression/R/Brier.survival.R | 64 riskRegression-2022.09.23/riskRegression/R/RcppExports.R | 16 riskRegression-2022.09.23/riskRegression/R/Score.R | 1497 +++++----- riskRegression-2022.09.23/riskRegression/R/computePerformance.R | 3 riskRegression-2022.09.23/riskRegression/R/crossvalPerf.R | 412 ++ riskRegression-2022.09.23/riskRegression/R/getInfluenceCurve.R | 144 riskRegression-2022.09.23/riskRegression/man/Score.Rd | 3 riskRegression-2022.09.23/riskRegression/src/RcppExports.cpp | 57 riskRegression-2022.09.23/riskRegression/src/arma-wrap.cpp | 34 riskRegression-2022.09.23/riskRegression/src/arma-wrap.h | 3 riskRegression-2022.09.23/riskRegression/src/getInfluenceFunctionAUC.cpp | 391 -- riskRegression-2022.09.23/riskRegression/src/getInfluenceFunctionBrier.cpp | 161 - riskRegression-2022.09.23/riskRegression/vignettes/IFAUC.Rmd | 110 riskRegression-2022.09.23/riskRegression/vignettes/IFBrier.Rmd | 29 20 files changed, 1417 insertions(+), 1733 deletions(-)
More information about riskRegression at CRAN
Permanent link
Title: LS-TreeBoost and LAD-TreeBoost for Gene Regulatory Network
Reconstruction
Description: Provides an implementation of Regularized LS-TreeBoost & LAD-TreeBoost algorithm for Regulatory Network inference from any type of expression data (Microarray/RNA-seq etc).
Author: Raghvendra Mall [aut, cre],
Khalid Kunji [aut],
Melissa O'Neill [ctb]
Maintainer: Raghvendra Mall <raghvendra5688@gmail.com>
Diff between RGBM versions 1.0-9 dated 2022-08-11 and 1.0-10 dated 2022-09-26
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/train_regression_stump.cpp | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: A Framework for Robust Shiny Applications
Description: An opinionated framework for building a production-ready
'Shiny' application. This package contains a series of tools for
building a robust 'Shiny' application from start to finish.
Author: Colin Fay [cre, aut] ,
Vincent Guyader [aut] ,
Sebastien Rochette [aut] ,
Cervan Girard [aut] ,
Novica Nakov [ctb],
David Granjon [ctb],
Arthur Breant [ctb],
Antoine Languillaume [ctb],
ThinkR [cph]
Maintainer: Colin Fay <contact@colinfay.me>
Diff between golem versions 0.3.3 dated 2022-07-13 and 0.3.4 dated 2022-09-26
DESCRIPTION | 10 +++---- MD5 | 34 ++++++++++++------------- R/add_dockerfiles.R | 10 +++---- R/add_r_files.R | 1 R/modules_fn.R | 1 R/test_helpers.R | 5 --- R/with_opt.R | 42 +++++++++++++++---------------- inst/doc/a_start.html | 4 +- inst/doc/b_dev.html | 4 +- inst/doc/c_deploy.html | 4 +- inst/doc/d_js.html | 4 +- inst/doc/e_config.html | 2 - man/dockerfiles.Rd | 10 +++---- man/get_golem_options.Rd | 42 +++++++++++++++---------------- man/testhelpers.Rd | 4 -- tests/testthat/test-add_deploy_helpers.R | 5 ++- tests/testthat/test-extra_sysreqs.R | 3 ++ tests/testthat/test-renv_stuff.R | 4 ++ 18 files changed, 93 insertions(+), 96 deletions(-)
Title: Ridgeline Plots in 'ggplot2'
Description: Ridgeline plots provide a convenient way of visualizing changes in distributions over time or space. This package enables the creation of such plots in 'ggplot2'.
Author: Claus O. Wilke [aut, cre]
Maintainer: Claus O. Wilke <wilke@austin.utexas.edu>
Diff between ggridges versions 0.5.3 dated 2021-01-08 and 0.5.4 dated 2022-09-26
DESCRIPTION | 13 MD5 | 36 +- NAMESPACE | 1 NEWS.md | 5 R/geoms-gradient.R | 13 R/geoms.R | 14 R/geomsv.R | 14 R/ggridges.R | 1 R/position.R | 9 R/stats.R | 5 R/utils.R | 1 README.md | 36 +- build/vignette.rds |binary inst/doc/gallery.html | 288 ++++++++++---------- inst/doc/introduction.html | 648 +++++++++++++++++++++++++++------------------ man/ggridges.Rd | 1 man/position_raincloud.Rd | 10 man/reduce.Rd | 1 man/stat_binline.Rd | 17 - 19 files changed, 655 insertions(+), 458 deletions(-)
Title: Clustering on Network of Samples
Description: Wires together large collections of single-cell RNA-seq datasets, which allows for both the identification of recurrent cell clusters and the propagation of information between datasets in multi-sample or atlas-scale collections. 'Conos' focuses on the uniform mapping of homologous cell types across heterogeneous sample collections. For instance, users could investigate a collection of dozens of peripheral blood samples from cancer patients combined with dozens of controls, which perhaps includes samples of a related tissue such as lymph nodes. This package interacts with data available through the 'conosPanel' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/kharchenkolab/conos>. The size of the 'conosPanel' package is approximately 12 MB.
Author: Viktor Petukhov [aut],
Nikolas Barkas [aut],
Peter Kharchenko [aut],
Weiliang Qiu [ctb],
Evan Biederstedt [aut, cre]
Maintainer: Evan Biederstedt <evan.biederstedt@gmail.com>
Diff between conos versions 1.4.7 dated 2022-09-04 and 1.4.8 dated 2022-09-26
DESCRIPTION | 14 ++-- MD5 | 25 ++++---- NAMESPACE | 2 R/RcppExports.R | 4 + R/communities.R | 1 R/integrations.R | 93 ++++++++++++++++++++++++++++++ README.md | 2 man/Conos.Rd | 90 ++++++++++++++--------------- man/armaCor.Rd |only man/filter.genes.by.cluster.expression.Rd |only man/plotEmbeddings.Rd | 10 --- man/plotSamples.Rd | 10 --- man/velocityInfoConos.Rd |only src/RcppExports.cpp | 12 +++ src/spcov.cpp | 17 +++++ 15 files changed, 198 insertions(+), 82 deletions(-)